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[Morphology][Tasks] introduce generic fillholes algorithm #119

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[Morphology][Tasks] introduce generic fillholes algorithm #119

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1a72d8f
[Morphology][Tasks] introduce generic fillholes algorithm
tretornaz Jan 4, 2023
773a632
[Morphology][fillholes] follow review request
tretornaz Feb 12, 2023
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14 changes: 12 additions & 2 deletions benchmark/benchmarks.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
Expand Down Expand Up @@ -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
8 changes: 6 additions & 2 deletions src/ImageMorphology.jl
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Expand Up @@ -24,6 +24,7 @@ include("connected.jl")
include("clearborder.jl")
include("extreme_filter.jl")
include("extremum.jl")
include("fillholes.jl")
include("ops/dilate.jl")
include("ops/erode.jl")
include("ops/closing.jl")
Expand Down Expand Up @@ -129,8 +130,10 @@ export

#feature_transform.jl
feature_transform,
distance_transform,
clearborder,
distance_transform, clearborder,

fillhole,
fillhole!,

#leveling
low_leveling,
Expand All @@ -139,6 +142,7 @@ export
high_leveling!,
leveling,
leveling!,

#extremum
hmaxima,
hmaxima!,
Expand Down
58 changes: 58 additions & 0 deletions src/fillholes.jl
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@@ -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
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@johnnychen94 johnnychen94 Feb 15, 2023 •
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For generic programming: tmp[i] = zero(T) where I assume T = eltype(img)

The difference is very small but noteworthy:

  • tmp[i] = 0 would be valid if there's a conversion from 0 (Int) to eltype(tmp)
  • tmp[i] = zero(T) would be valid as long as zero(T) is defined (which is true for almost all number-like types)

Why we should prefer the zero(T) version is that: not all types (should) support (implicit) conversion from Int. The following is an JuliaImages example, but you can quickly come up with many like it:

julia> using ImageCore

julia> zero(HSV)
HSV{Float32}(0.0f0,0.0f0,0.0f0)

julia> HSV(0)
ERROR: in ccolor, no automatic conversion from Int64 and HSV
Stacktrace:
 [1] ccolor(#unused#::Type{HSV}, #unused#::Type{Int64})
   @ ColorTypes ~/.julia/packages/ColorTypes/1dGw6/src/traits.jl:410
 [2] convert(#unused#::Type{HSV}, c::Int64)
   @ ColorTypes ~/.julia/packages/ColorTypes/1dGw6/src/conversions.jl:74
 [3] HSV(x::Int64)
   @ ColorTypes ~/.julia/packages/ColorTypes/1dGw6/src/types.jl:464
 [4] top-level scope
   @ REPL[3]:1

end

return mreconstruct!(erode, out, tmp, img, se)
end
135 changes: 135 additions & 0 deletions test/fillholes.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,135 @@
@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
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Could you add a test where the 0s at the border are not a single connected component? Also the case where there are no zeros on the border m. Also add a test for multiple interior holes.

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Fixed

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Note that we could say nothing for "holes" in the border, anyway we don't have acess to underlyting image domain, are these really holes
So as other image processing framework we don't fill hole touching the borders

]

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)
fillhole!(out, img)
@test out == expected

# in place diamond
out = similar(img)
fillhole!(out, img, strel_diamond((3, 3)))
@test out == expected

# more holes
#binary
img = Bool[
0 0 0 0 0 1 1 0
0 1 1 1 0 0 0 0
0 1 0 1 0 0 0 0
0 1 1 1 0 0 0 0
0 0 0 1 1 1 0 0
1 0 0 1 0 1 0 0
1 0 0 1 1 1 0 0
1 0 0 0 0 0 0 0
]

expected = Bool[
0 0 0 0 0 1 1 0
0 1 1 1 0 0 0 0
0 1 1 1 0 0 0 0
0 1 1 1 0 0 0 0
0 0 0 1 1 1 0 0
1 0 0 1 1 1 0 0
1 0 0 1 1 1 0 0
1 0 0 0 0 0 0 0
]

out = fillhole(img)
@test eltype(out) == Bool
@test out == expected

# in place
out = similar(img)
fillhole!(out, img)
@test out == expected


# "holes" touching the borders
# by definitions we can't say anything in this case
# because we have no acess to the underlying image domain
# so like other framework, leave these holes not filled

#binary
img = Bool[
0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1
0 0 0 0 0 0 1 0
0 0 0 0 0 0 1 0
1 1 1 1 0 0 1 1
1 0 0 1 0 0 0 0
1 1 1 1 0 0 0 0
1 0 0 0 0 0 0 0
]

expected = Bool[
0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1
0 0 0 0 0 0 1 0
0 0 0 0 0 0 1 0
1 1 1 1 0 0 1 1
1 1 1 1 0 0 0 0
1 1 1 1 0 0 0 0
1 0 0 0 0 0 0 0
]

out = fillhole(img)
@test eltype(out) == Bool
@test out == expected

# in place
out = similar(img)
fillhole!(out, img)
@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)
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Add a test for an OffsetArray. Either check for the appropriate exception or correct function.


end
1 change: 1 addition & 0 deletions test/runtests.jl
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Expand Up @@ -37,6 +37,7 @@ include("testutils.jl")
include("feature_transform.jl")
include("leveling.jl")
include("clearborder.jl")
include("fillholes.jl")
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Why is this indented?

@info "Beginning deprecation tests, warnings are expected"
include("deprecations.jl")
end
Expand Down