Skip to content

add a DiskArrays extension so that Zarr arrays are fast #136

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft

add a DiskArrays extension so that Zarr arrays are fast #136

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9b88923
bump minimum julia to 1.10 the current LTS
bjarthur Mar 11, 2025
6820606
add a fast path for chunked arrays
bjarthur Mar 11, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 8 additions & 1 deletion Project.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,22 @@ OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
TiledIteration = "06e1c1a7-607b-532d-9fad-de7d9aa2abac"

[weakdeps]
DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"

[extensions]
DiskArraysExt = "DiskArrays"

[compat]
DataStructures = "0.17.11, 0.18"
DiskArrays = "0.4"
Documenter = "0.24, 0.25, 0.26, 0.27"
ImageCore = "0.9, 0.10"
LoopVectorization = "0.12"
OffsetArrays = "1.9"
Requires = "1"
TiledIteration = "0.3.1, 0.4, 0.5"
julia = "1.6"
julia = "1.10"

[extras]
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Expand Down
38 changes: 38 additions & 0 deletions ext/DiskArraysExt.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
module DiskArraysExt

using ImageMorphology, DiskArrays

get_extreme_value(::typeof(max), ::Type{T}) where {T} = typemin(T)
get_extreme_value(::typeof(min), ::Type{T}) where {T} = typemax(T)

function ImageMorphology.extreme_filter!(f, out, A::AbstractDiskArray, Ω)
axes(out) == axes(A) || throw(DimensionMismatch("axes(out) must match axes(A)"))
ImageMorphology.require_select_function(f, eltype(A))
val0 = get_extreme_value(f, eltype(A))

pad = extrema.(axes(Ω))
PAD1 = CartesianIndex(ntuple(i->pad[i][1], length(pad)))
PAD2 = CartesianIndex(ntuple(i->pad[i][2], length(pad)))
ZERO = CartesianIndex(ntuple(_->0, ndims(A)))
ONE = CartesianIndex(ntuple(_->1, ndims(A)))
SIZEA = CartesianIndex(size(A))
chunk_pad = [c+length(range(p...))-1
for (c,p) in zip(DiskArrays.max_chunksize(eachchunk(A)),pad)]
A_chunk = Array{eltype(A)}(undef, chunk_pad...)
out_chunk = similar(A_chunk)
for i in eachchunk(A)
I = minimum(CartesianIndices(i))
R = maximum(CartesianIndices(i))
A_chunk .= val0
A1 = max(ONE, I+PAD1)
A2 = min(SIZEA, R+PAD2)
A_chunk[ONE:A2-A1+ONE] .= A[A1:A2]
ImageMorphology._extreme_filter!(strel_type(Ω), f, out_chunk, A_chunk, Ω)
OUT1 = ONE-PAD1 + min(ZERO, I+PAD1-ONE)
OUT2 = OUT1+R-I
out[I:R] .= out_chunk[OUT1:OUT2]
end
return out
end

end
Loading