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Merged
merged 6 commits into from
May 13, 2025
Merged

Add functionality to use arbitrary singular values in ConcatDiskArrays #256

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9add95a
Add test case for zero fill concatdiskarray
Apr 11, 2025
b744d4f
Enable arbitrary single values in concatDiskArray
Apr 11, 2025
2284968
Update src/cat.jl
felixcremer Apr 12, 2025
eaadc95
Update src/cat.jl
felixcremer Apr 12, 2025
afe15cc
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felixcremer Apr 12, 2025
6781eae
Wrap fill values in MissingTile for ConcatDiskArray
May 13, 2025
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31 changes: 16 additions & 15 deletions src/cat.jl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

"""
ConcatDiskArray <: AbstractDiskArray

Expand All @@ -15,7 +14,7 @@ Returned from `cat` on disk arrays.

It is also useful on its own as it can easily concatenate an array of disk arrays.
"""
struct ConcatDiskArray{T,N,P,C,HC,ID} <: AbstractDiskArray{T,N}
struct ConcatDiskArray{T,N,P,C,HC, ID} <: AbstractDiskArray{T,N}
parents::P
startinds::NTuple{N,Vector{Int}}
size::NTuple{N,Int}
Expand All @@ -24,23 +23,25 @@ struct ConcatDiskArray{T,N,P,C,HC,ID} <: AbstractDiskArray{T,N}
innerdims::Val{ID}
end

function ConcatDiskArray(arrays::AbstractArray{Union{<:AbstractArray,Missing}})
function ConcatDiskArray(arrays::AbstractArray{Union{<:AbstractArray,Missing}}; fill=missing)
et = Base.nonmissingtype(eltype(arrays))
T = Union{Missing,eltype(et)}
T = promotetype(typeof(fill), eltype(et))
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@rafaqz rafaqz Apr 12, 2025 •
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I thought the passed in array would still contain either arrays or missing values, but we would just return fill for those sections, so fill would need to be a struct field.

So what we have here is kinda half way. Probably we should either drop the fill keyword (and just rely on the array values) or keep it as a struct field and use missing in the array.

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I prefer to drop the fill keyword. I actual thought I already did so.
With my approach we can have different fill values in different parts of the concatenated array.

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But is that actually useful? I can't imagine a real use case for multiple fill values. And putting missing in the array seems clearer for representing missing arrays.

The missing value used in the array of arrays doesn't have to be coupled to the fill value.

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I agree that it might be a bit dangerous to allow arbitrary values to represent missings. OTOH one never knows when this might become useful for some reason. I am ok with both ways and would currently slightly prefer @felixcremer s solution because there is already an implementation. If we want to be a bit more on the safe side, we could introduce a small wrapper type like

struct MissingTile{F}
    fillvalue::F
end

that explicitly marks missing entries to be concatenated and how they should be filled. The main reason why the current solution might be problematic is for DiskArrays with arrays as eltype, but maybe this is overthinking things a bit too much.

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Suggested change
T = promotetype(typeof(fill), eltype(et))
T = Union{Missing,eltype(et)}

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@rafaqz rafaqz Apr 14, 2025 •
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Don't you have to read all the fill values in the array and promote them? Missing is not necessarily in the type?

N = ndims(arrays)
M = ndims(et)
_ConcatDiskArray(arrays, T, Val(N), Val(M))
end

function infer_eltypes(arrays)
foldl(arrays, init=(-1, Union{})) do (M, T), a
if ismissing(a)
(M, promote_type(Missing, T))
if !isa(a, AbstractArray)
(M, promote_type(typeof(a), T))
else
M == -1 || ndims(a) == M || throw(ArgumentError("All arrays to concatenate must have equal ndims"))
(ndims(a), promote_type(eltype(a), T))
end
end
end

function ConcatDiskArray(arrays::AbstractArray{<:AbstractArray})
N = ndims(arrays)
T = eltype(eltype(arrays))
Expand Down Expand Up @@ -90,7 +91,7 @@ function arraysize_and_startinds(arrays1)
sizes = map(i -> zeros(Int, i), size(arrays1))
for i in CartesianIndices(arrays1)
ai = arrays1[i]
ismissing(ai) && continue
ai isa AbstractArray || continue
sizecur = extenddims(size(ai), size(arrays1), 1)
foreach(sizecur, i.I, sizes) do si, ind, sizeall
if sizeall[ind] == 0
Expand Down Expand Up @@ -123,10 +124,10 @@ function readblock!(a::ConcatDiskArray, aout, inds::AbstractUnitRange...)
# Find affected blocks and indices in blocks
_concat_diskarray_block_io(a, inds...) do outer_range, array_range, I
vout = view(aout, outer_range...)
if ismissing(I)
vout .= missing
else
if I isa CartesianIndex
readblock!(a.parents[I], vout, array_range...)
else
vout .= I
end
end
end
Expand Down Expand Up @@ -170,10 +171,10 @@ function _concat_diskarray_block_io(f, a::ConcatDiskArray, inds...)
#Shorten array range to shape of actual array
array_range = ntuple(j -> array_range[j], ID)
outer_range = fix_outerrangeshape(outer_range, array_range)
if ismissing(myar)
f(outer_range, array_range, missing)
else
if myar isa AbstractArray
f(outer_range, array_range, cI)
else
f(outer_range, array_range, myar)
end
end
end
Expand All @@ -189,13 +190,13 @@ function concat_chunksize(parents)
newchunks = map(s -> Vector{Union{RegularChunks,IrregularChunks}}(undef, s), size(parents))
for i in CartesianIndices(parents)
array = parents[i]
ismissing(array) && continue
!isa(array,AbstractArray) && continue
chunks = eachchunk(array)
foreach(chunks.chunks, i.I, newchunks) do c, ind, newc
if !isassigned(newc, ind)
newc[ind] = c
elseif c != newc[ind]
throw(ArgumentError("Chunk sizes don't forma grid"))
throw(ArgumentError("Chunk sizes don't form a grid"))
end
end
end
Expand Down
29 changes: 29 additions & 0 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -492,6 +492,34 @@ end
@test slic == Float64[1, 2, 3, 4, 1, 2, 3, 4]
end

@testset "Concat DiskArray with fill zero tiles" begin
a = zeros(Int, 3, 4)
b = ones(Int, 2, 4)
c = fill(2, 3, 5)
d = fill(0, 2, 5)
aconc = DiskArrays.ConcatDiskArray(reshape([a, b, c, 0], 2, 2))
abase = [a c; b d]
@test all(isequal.(aconc[:, :], abase))
@test all(isequal.(aconc[3:4, 4:6], abase[3:4, 4:6]))
ch = DiskArrays.eachchunk(aconc)
@test ch.chunks[1] == [1:3, 4:5]
@test ch.chunks[2] == [1:4, 5:9]

a = ones(100, 50)
b = [rem(i.I[3], 5) == 0 ? 0 : a for i in CartesianIndices((1, 1, 100))]
b[1] = 0
a_conc = DiskArrays.ConcatDiskArray(b)
ch = eachchunk(a_conc)
@test ch.chunks[1] == [1:100]
@test ch.chunks[2] == [1:50]
@test ch.chunks[3] === DiskArrays.RegularChunks(1, 0, 100)

@test all(isequal.(a_conc[2, 2, 1:5], [0, 1.0, 1.0, 1.0, 0]))
@test all(isequal.(a_conc[end, end, 95:100], [0, 1.0, 1.0, 1.0, 1.0, 0]))

end


@testset "Concat DiskArray with missing tiles" begin
a = zeros(Int, 3, 4)
b = ones(Int, 2, 4)
Expand All @@ -518,6 +546,7 @@ end
@test all(isequal.(a_conc[end, end, 95:100], [missing, 1.0, 1.0, 1.0, 1.0, missing]))

end

end

@testset "Broadcast with length 1 and 0 final dim" begin
Expand Down