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StructArrays

Efficient implementation of struct arrays in Julia

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StructArrays

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This package introduces the type StructArray which is an AbstractArray whose elements are struct (for example NamedTuples, or ComplexF64, or a custom user defined struct). While a StructArray iterates structs, the layout is column based (meaning each field of the struct is stored in a separate Array).

Base.getproperty or the dot syntax can be used to access columns, whereas rows can be accessed with getindex.

The package was largely inspired by the Columns type in IndexedTables which it now replaces.

Example usage to store complex numbers

julia> using StructArrays, Random

julia> Random.seed!(4);

julia> s = StructArray{ComplexF64}((rand(2,2), rand(2,2)))
2×2 StructArray(::Array{Float64,2}, ::Array{Float64,2}) with eltype Complex{Float64}:
 0.680079+0.625239im   0.92407+0.267358im
 0.874437+0.737254im  0.929336+0.804478im

julia> s[1, 1]
0.680079235935741 + 0.6252391193298537im

julia> s.re
2×2 Array{Float64,2}:
 0.680079  0.92407
 0.874437  0.929336

julia> StructArrays.components(s) # obtain all field arrays as a named tuple
(re = [0.680079 0.92407; 0.874437 0.929336], im = [0.625239 0.267358; 0.737254 0.804478])

Note that the same approach can be used directly from an Array of complex numbers:

julia> StructArray([1+im, 3-2im])
2-element StructArray(::Array{Int64,1}, ::Array{Int64,1}) with eltype Complex{Int64}:
 1 + 1im
 3 - 2im

Collection and initialization

One can also create a StructArray from an iterable of structs without creating an intermediate Array:

julia> StructArray(log(j+2.0*im) for j in 1:10)
10-element StructArray(::Array{Float64,1}, ::Array{Float64,1}) with eltype Complex{Float64}:
 0.8047189562170501 + 1.1071487177940904im
 1.0397207708399179 + 0.7853981633974483im
 1.2824746787307684 + 0.5880026035475675im
 1.4978661367769954 + 0.4636476090008061im
  1.683647914993237 + 0.3805063771123649im
 1.8444397270569681 + 0.3217505543966422im
  1.985145956776061 + 0.27829965900511133im
 2.1097538525880535 + 0.24497866312686414im
 2.2213256282451583 + 0.21866894587394195im
 2.3221954495706862 + 0.19739555984988078im

Another option is to create an uninitialized StructArray and then fill it with data. Just like in normal arrays, this is done with the undef syntax:

julia> s = StructArray{ComplexF64}(undef, 2, 2)
2×2 StructArray(::Array{Float64,2}, ::Array{Float64,2}) with eltype Complex{Float64}:
 6.91646e-310+6.91646e-310im  6.91646e-310+6.91646e-310im
 6.91646e-310+6.91646e-310im  6.91646e-310+6.91646e-310im

julia> rand!(s)
2×2 StructArray(::Array{Float64,2}, ::Array{Float64,2}) with eltype Complex{Float64}:
 0.680079+0.874437im  0.625239+0.737254im
  0.92407+0.929336im  0.267358+0.804478im

Using custom array types

StructArrays supports using custom array types. It is always possible to pass field arrays of a custom type. The "custom array of structs to struct of custom arrays" transformation will use the similar method of the custom array type. This can be useful when working on the GPU for example:

julia> using StructArrays, CuArrays

julia> a = CuArray(rand(Float32, 10));

julia> b = CuArray(rand(Float32, 10));

julia> StructArray{ComplexF32}((a, b))
10-element StructArray(::CuArray{Float32,1}, ::CuArray{Float32,1}) with eltype Complex{Float32}:
  0.19555175f0 + 0.9604322f0im
  0.68348145f0 + 0.5778245f0im
  0.69664395f0 + 0.79825306f0im
 0.118531585f0 + 0.3031248f0im
  0.80057466f0 + 0.8964418f0im
  0.63772964f0 + 0.2923274f0im
  0.65374136f0 + 0.7932533f0im
   0.6043732f0 + 0.65964353f0im
   0.1106627f0 + 0.090207934f0im
    0.707458f0 + 0.1700114f0im

julia> c = CuArray(rand(ComplexF32, 10));

julia> StructArray(c)
10-element StructArray(::Array{Float32,1}, ::Array{Float32,1}) with eltype Complex{Float32}:
  0.7176411f0 + 0.864058f0im
   0.252609f0 + 0.14824867f0im
 0.26842773f0 + 0.9084332f0im
 0.33128333f0 + 0.5106474f0im
  0.6509278f0 + 0.87059164f0im
  0.9522146f0 + 0.053706646f0im
   0.899577f0 + 0.63242567f0im
   0.325814f0 + 0.59225655f0im
 0.56267905f0 + 0.21927536f0im
 0.49719965f0 + 0.754143f0im

If you already have your data in a StructArray with field arrays of a given format (say plain Array) you can change them with replace_storage:

julia> s = StructArray([1.0+im, 2.0-im])
2-element StructArray(::Array{Float64,1}, ::Array{Float64,1}) with eltype Complex{Float64}:
 1.0 + 1.0im
 2.0 - 1.0im

julia> replace_storage(CuArray, s)
2-element StructArray(::CuArray{Float64,1}, ::CuArray{Float64,1}) with eltype Complex{Float64}:
 1.0 + 1.0im
 2.0 - 1.0im

Example usage to store a data table

julia> t = StructArray((a = [1, 2], b = ["x", "y"]))
2-element StructArray(::Array{Int64,1}, ::Array{String,1}) with eltype NamedTuple{(:a, :b),Tuple{Int64,String}}:
 (a = 1, b = "x")
 (a = 2, b = "y")

julia> t[1]
(a = 1, b = "x")

julia> t.a
2-element Array{Int64,1}:
 1
 2

julia> push!(t, (a = 3, b = "z"))
3-element StructArray(::Array{Int64,1}, ::Array{String,1}) with eltype NamedTuple{(:a, :b),Tuple{Int64,String}}:
 (a = 1, b = "x")
 (a = 2, b = "y")
 (a = 3, b = "z")

Lazy row iteration

StructArrays also provides a LazyRow wrapper for lazy row iteration. LazyRow(t, i) does not materialize the i-th row but returns a lazy wrapper around it on which getproperty does the correct thing. This is useful when the row has many fields only some of which are necessary. It also allows changing columns in place.

julia> t = StructArray((a = [1, 2], b = ["x", "y"]));

julia> LazyRow(t, 2).a
2

julia> LazyRow(t, 2).a = 123
123

julia> t
2-element StructArray(::Array{Int64,1}, ::Array{String,1}) with eltype NamedTuple{(:a, :b),Tuple{Int64,String}}:
 (a = 1, b = "x")
 (a = 123, b = "y")

To iterate in a lazy way one can simply iterate LazyRows:

julia> map(t -> t.b ^ t.a, LazyRows(t))
2-element Array{String,1}:
 "x"
 "yy"

Advanced: structures with non-standard data layout

StructArrays support structures with custom data layout. The user is required to overload staticschema in order to define the custom layout, component to access fields of the custom layout, and createinstance(T, fields...) to create an instance of type T from its custom fields fields. In other word, given x::T, createinstance(T, (component(x, f) for f in fieldnames(staticschema(T)))...) should successfully return an instance of type T.

Here is an example of a type MyType that has as custom fields either its field data or fields of its field rest (which is a named tuple):

using StructArrays

struct MyType{T, NT<:NamedTuple}
    data::T
    rest::NT
end

MyType(x; kwargs...) = MyType(x, values(kwargs))

function StructArrays.staticschema(::Type{MyType{T, NamedTuple{names, types}}}) where {T, names, types}
    return NamedTuple{(:data, names...), Base.tuple_type_cons(T, types)}
end

function StructArrays.component(m::MyType, key::Symbol)
    return key === :data ? getfield(m, 1) : getfield(getfield(m, 2), key)
end

# generate an instance of MyType type
function StructArrays.createinstance(::Type{MyType{T, NT}}, x, args...) where {T, NT}
    return MyType(x, NT(args))
end

s = [MyType(rand(), a=1, b=2) for i in 1:10]
StructArray(s)

In the above example, our MyType was composed of data of type Float64 and rest of type NamedTuple. In many practical cases where there are custom types involved it's hard for StructArrays to automatically widen the types in case they are heterogeneous. The following example demonstrates a widening method in that scenario.

using Tables

# add a source of custom type data
struct Location{U}
    x::U
    y::U
end
struct Region{V}
    area::V
end

s1 = MyType(Location(1, 0), place = "Delhi", rainfall = 200)
s2 = MyType(Location(2.5, 1.9), place = "Mumbai", rainfall = 1010)
s3 = MyType(Region([Location(1, 0), Location(2.5, 1.9)]), place = "North India", rainfall = missing)

s = [s1, s2, s3]
# Now if we try to do StructArray(s)
# we will get an error

function meta_table(iter)
    cols = Tables.columntable(iter)
    meta_table(first(cols), Base.tail(cols)) 
end

function meta_table(data, rest::NT) where NT<:NamedTuple
    F = MyType{eltype(data), StructArrays.eltypes(NT)}
    return StructArray{F}(; data=data, rest...)
end

meta_table(s)

The above strategy has been tested and implemented in GeometryBasics.jl.

Advanced: mutate-or-widen style accumulation

StructArrays provides a function StructArrays.append!!(dest, src) (unexported) for "mutate-or-widen" style accumulation. This function can be used via BangBang.append!! and BangBang.push!! as well.

StructArrays.append!! works like append!(dest, src) if dest can contain all element types in src iterator; i.e., it mutates dest in-place:

julia> dest = StructVector((a=[1], b=[2]))
1-element StructArray(::Array{Int64,1}, ::Array{Int64,1}) with eltype NamedTuple{(:a, :b),Tuple{Int64,Int64}}:
 (a = 1, b = 2)

julia> StructArrays.append!!(dest, [(a = 3, b = 4)])
2-element StructArray(::Array{Int64,1}, ::Array{Int64,1}) with eltype NamedTuple{(:a, :b),Tuple{Int64,Int64}}:
 (a = 1, b = 2)
 (a = 3, b = 4)

julia> ans === dest
true

Unlike append!, append!! can also widen element type of dest array:

julia> StructArrays.append!!(dest, [(a = missing, b = 6)])
3-element StructArray(::Array{Union{Missing, Int64},1}, ::Array{Int64,1}) with eltype NamedTuple{(:a, :b),Tuple{Union{Missing, Int64},Int64}}:
 NamedTuple{(:a, :b),Tuple{Union{Missing, Int64},Int64}}((1, 2))
 NamedTuple{(:a, :b),Tuple{Union{Missing, Int64},Int64}}((3, 4))
 NamedTuple{(:a, :b),Tuple{Union{Missing, Int64},Int64}}((missing, 6))

julia> ans === dest
false

Since the original array dest cannot hold the input, a new array is created (ans !== dest).

Combined with function barriers, append!! is a useful building block for implementing collect-like functions.

Advanced: using StructArrays in CUDA kernels

It is possible to combine StructArrays with CUDAnative, in order to create CUDA kernels that work on StructArrays directly on the GPU. Make sure you are familiar with the CUDAnative documentation (esp. kernels with plain CuArrays) before experimenting with kernels based on StructArrays.

using CUDAnative, CuArrays, StructArrays
d = StructArray(a = rand(100), b = rand(100))

# move to GPU
dd = replace_storage(CuArray, d)
de = similar(dd)

# a simple kernel, to copy the content of `dd` onto `de`
function kernel!(dest, src)
    i = (blockIdx().x-1)*blockDim().x + threadIdx().x
    if i <= length(dest)
        dest[i] = src[i]
    end
    return nothing
end

threads = 1024
blocks = cld(length(dd),threads)

@cuda threads=threads blocks=blocks kernel!(de, dd)

Applying a function on each field array

julia> struct Foo
       a::Int
       b::String
       end

julia> s = StructArray([Foo(11, "a"), Foo(22, "b"), Foo(33, "c"), Foo(44, "d"), Foo(55, "e")]);

julia> s
5-element StructArray(::Vector{Int64}, ::Vector{String}) with eltype Foo:
 Foo(11, "a")
 Foo(22, "b")
 Foo(33, "c")
 Foo(44, "d")
 Foo(55, "e")

julia> StructArrays.foreachfield(v -> deleteat!(v, 3), s)

julia> s
4-element StructArray(::Vector{Int64}, ::Vector{String}) with eltype Foo:
 Foo(11, "a")
 Foo(22, "b")
 Foo(44, "d")
 Foo(55, "e")

First Commit

04/19/2018

Last Touched

1 day ago

Commits

180 commits