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methods.jl
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methods.jl
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# Array info
for (m, f) in ((:Base, :size), (:Base, :axes), (:Base, :firstindex), (:Base, :lastindex))
@eval begin
@inline $m.$f(A::AbstractBasicDimArray, dims::AllDims) = $m.$f(A, dimnum(A, dims))
end
end
# Reducing methods
# With a function arg version
for (m, f) in ((:Base, :sum), (:Base, :prod), (:Base, :maximum), (:Base, :minimum),
(:Base, :extrema), (:Statistics, :mean))
_f = Symbol('_', f)
@eval begin
# Base methods
@inline $m.$f(A::AbstractDimArray; dims=:, kw...) = $_f(A, dims; kw...)
@inline $m.$f(f, A::AbstractDimArray; dims=:, kw...) = $_f(f, A, dims; kw...)
# Local dispatch methods
# - Return a reduced DimArray
@inline $_f(A::AbstractDimArray, dims; kw...) =
rebuild(A, $m.$f(parent(A); dims=dimnum(A, _astuple(dims)), kw...), reducedims(A, dims))
@inline $_f(f, A::AbstractDimArray, dims; kw...) =
rebuild(A, $m.$f(f, parent(A); dims=dimnum(A, _astuple(dims)), kw...), reducedims(A, dims))
# - Return a scalar
@inline $_f(A::AbstractDimArray, dims::Colon; kw...) = $m.$f(parent(A); dims, kw...)
@inline $_f(f, A::AbstractDimArray, dims::Colon; kw...) = $m.$f(f, parent(A); dims, kw...)
end
end
# With no function arg version
for (m, f) in ((:Statistics, :std), (:Statistics, :var))
_f = Symbol('_', f)
@eval begin
# Base methods
$m.$f(A::AbstractDimArray; corrected::Bool=true, mean=nothing, dims=:) =
$_f(A, corrected, mean, dims)
# Local dispatch methods - Returns a reduced array
@inline $_f(A::AbstractDimArray, corrected, mean, dims) =
rebuild(A, $m.$f(parent(A); corrected=corrected, mean=mean, dims=dimnum(A, _astuple(dims))), reducedims(A, dims))
# - Returns a scalar
@inline $_f(A::AbstractDimArray, corrected, mean, dims::Colon) =
$m.$f(parent(A); corrected=corrected, mean=mean, dims=:)
end
end
for (m, f) in ((:Statistics, :median), (:Base, :any), (:Base, :all))
_f = Symbol('_', f)
@eval begin
@inline $m.$f(A::AbstractDimArray; dims=:) = $_f(A, dims)
# Local dispatch methods - Returns a reduced array
@inline $_f(A::AbstractDimArray, dims) =
rebuild(A, $m.$f(parent(A); dims=dimnum(A, _astuple(dims))), reducedims(A, dims))
# - Returns a scalar
@inline $_f(A::AbstractDimArray, dims::Colon) = $m.$f(parent(A); dims=:)
end
end
function Base.mapreduce(f, op, A::AbstractDimArray; dims=Base.Colon(), kw...)
dims === Colon() && return mapreduce(f, op, parent(A); kw...)
rebuild(A, mapreduce(f, op, parent(A); dims=dimnum(A, dims), kw...), reducedims(A, dims))
end
# TODO: Unfortunately Base/accumulate.jl kw methods all force dims to be Integer.
# accumulate wont work unless that is relaxed, or we copy half of the file here.
# Base._accumulate!(op, B, A, dims::AllDims, init::Union{Nothing, Some}) =
# Base._accumulate!(op, B, A, dimnum(A, dims), init)
# Dimension dropping
function Base.dropdims(A::AbstractDimArray; dims)
dims = DD.dims(A, dims)
data = Base.dropdims(parent(A); dims=dimnum(A, dims))
rebuildsliced(A, data, _dropinds(A, dims))
end
@inline _dropinds(A, dims::Tuple) = dims2indices(A, map(d -> rebuild(d, 1), dims))
@inline _dropinds(A, dim::Dimension) = dims2indices(A, rebuild(dim, 1))
# Function application
function Base.map(f, As::AbstractDimArray...)
comparedims(As...)
newdata = map(f, map(parent, As)...)
rebuild(first(As); data=newdata)
end
@inline function Base.mapslices(f, A::AbstractDimArray; dims=1, kw...)
# Run `mapslices` on the parent array
dimnums = dimnum(A, _astuple(dims))
newdata = mapslices(f, parent(A); dims=dimnums, kw...)
ds = DD.dims(A, _astuple(dims))
# Run one slice with dimensions to get the transformed dim
d_inds = map(d -> rebuild(d, 1), otherdims(A, ds))
example_dims = length(d_inds) > 0 ? DD.dims(f(view(A, d_inds...))) : ()
replacement_dims = if isnothing(example_dims) || length(example_dims) != length(ds)
map(d -> rebuild(d, NoLookup()), ds)
else
example_dims
end
newdims = format(setdims(DD.dims(A), replacement_dims), newdata)
return rebuild(A, newdata, newdims)
end
"""
Base.eachslice(A::AbstractDimArray; dims,drop=true)
Create a generator that iterates over dimensions `dims` of `A`, returning arrays that
select all the data from the other dimensions in `A` using views.
The generator has `size` and `axes` equivalent to those of the provided `dims` if `drop=true`.
Otherwise it will have the same dimensionality as the underlying array with inner dimensions having size 1.
"""
@inline function Base.eachslice(A::AbstractDimArray; dims, drop=true)
dimtuple = _astuple(dims)
if !(dimtuple == ())
all(hasdim(A, dimtuple...)) || throw(DimensionMismatch("A doesn't have all dimensions $dims"))
end
_eachslice(A, dimtuple, drop)
end
Base.@constprop :aggressive function _eachslice(A::AbstractDimArray{T,N}, dims, drop) where {T,N}
slicedims = Dimensions.dims(A, dims)
Adims = Dimensions.dims(A)
if drop
ax = map(dim -> axes(A, dim), slicedims)
slicemap = map(Adims) do dim
hasdim(slicedims, dim) ? dimnum(slicedims, dim) : (:)
end
return Slices(A, slicemap, ax)
else
ax = map(Adims) do dim
hasdim(slicedims, dim) ? axes(A, dim) : axes(reducedims(dim, dim), 1)
end
slicemap = map(Adims) do dim
hasdim(slicedims, dim) ? dimnum(A, dim) : (:)
end
return Slices(A, slicemap, ax)
end
end
# works for arrays and for stacks
function _eachslice(x, dims::Tuple)
slicedims = Dimensions.dims(x, dims)
return (view(x, d...) for d in DimIndices(slicedims))
end
# These just return the parent for now
function Base.sort(A::AbstractDimVector; kw...)
newdims = (set(only(dims(A)), NoLookup()),)
newdata = sort(parent(A), kw...)
return rebuild(A, newdata, newdims)
end
function Base.sort(A::AbstractDimArray; dims, kw...)
newdata = sort(parent(A), dims=dimnum(A, dims), kw...)
replacement_dims = map(DD.dims(A, _astuple(dims))) do d
set(d, NoLookup())
end
newdims = setdims(DD.dims(A), replacement_dims)
return rebuild(A, newdata, newdims)
end
function Base.sortslices(A::AbstractDimArray; dims, kw...)
newdata = sortslices(parent(A), dims=dimnum(A, dims), kw...)
replacement_dims = map(DD.dims(A, _astuple(dims))) do d
set(d, NoLookup())
end
newdims = setdims(DD.dims(A), replacement_dims)
return rebuild(A, newdata, newdims)
end
Base.cumsum(A::AbstractDimVector) = rebuild(A, Base.cumsum(parent(A)))
Base.cumsum(A::AbstractDimArray; dims) = rebuild(A, cumsum(parent(A); dims=dimnum(A, dims)))
Base.cumsum!(B::AbstractArray, A::AbstractDimVector) = cumsum!(B, parent(A))
Base.cumsum!(B::AbstractArray, A::AbstractDimArray; dims) = cumsum!(B, parent(A); dims=dimnum(A, dims))
# Duplicated dims
for fname in (:cor, :cov)
@eval function Statistics.$fname(A::AbstractDimArray{<:Any,2}; dims=1, kw...)
newdata = Statistics.$fname(parent(A); dims=dimnum(A, dims), kw...)
removed_idx = dimnum(A, dims)
newrefdims = $dims(A)[removed_idx]
newdim = $dims(A)[3 - removed_idx]
rebuild(A, newdata, (newdim, newdim), (newrefdims,))
end
end
# Rotations
Base.rotl90(A::AbstractDimMatrix) = rebuild(A, rotl90(parent(A)), _rotdims_90(dims(A)))
function Base.rotl90(A::AbstractDimMatrix, k::Integer)
rebuild(A, rotl90(parent(A), k), _rotdims_k(dims(A), k))
end
Base.rotr90(A::AbstractDimMatrix) = rebuild(A, rotr90(parent(A)), _rotdims_270(dims(A)))
function Base.rotr90(A::AbstractDimMatrix, k::Integer)
rebuild(A, rotr90(parent(A), k), _rotdims_k(dims(A), -k))
end
Base.rot180(A::AbstractDimMatrix) = rebuild(A, rot180(parent(A)), _rotdims_180(dims(A)))
# Not type stable - but we have to lose type stability somewhere when
# dims are being swapped, by an Int value, so it may as well be here
function _rotdims_k(dims, k)
k = mod(k, 4)
k == 1 ? _rotdims_90(dims) :
k == 2 ? _rotdims_180(dims) :
k == 3 ? _rotdims_270(dims) : dims
end
_rotdims_90((dim_a, dim_b)) = reverse(dim_b), dim_a
_rotdims_180((dim_a, dim_b)) = reverse(dim_a), reverse(dim_b)
_rotdims_270((dim_a, dim_b)) = dim_b, reverse(dim_a)
# Dimension reordering
for (pkg, fname) in [(:Base, :permutedims), (:Base, :adjoint),
(:Base, :transpose), (:LinearAlgebra, :Transpose)]
@eval begin
@inline $pkg.$fname(A::AbstractDimArray{<:Any,2}) =
rebuild(A, $pkg.$fname(parent(A)), reverse(dims(A)))
@inline $pkg.$fname(A::AbstractDimArray{<:Any,1}) =
rebuild(A, $pkg.$fname(parent(A)), (AnonDim(NoLookup(Base.OneTo(1))), dims(A)...))
end
end
@inline function Base.permutedims(A::AbstractDimArray, perm)
rebuild(A, permutedims(parent(A), dimnum(A, Tuple(perm))), sortdims(dims(A), Tuple(perm)))
end
@inline function Base.PermutedDimsArray(A::AbstractDimArray{T,N}, perm) where {T,N}
perm_inds = dimnum(A, Tuple(perm))
iperm_inds = invperm(perm_inds)
data = parent(A)
data_perm = PermutedDimsArray{T,N,perm_inds,iperm_inds,typeof(data)}(data)
rebuild(A, data_perm, sortdims(dims(A), Tuple(perm)))
end
# Concatenation
Base.cat(A1::AbstractDimArray, As::AbstractDimArray...; dims) = _cat(dims, A1, As...)
function _cat(catdim::Union{Int,Symbol,DimOrDimType}, A1::AbstractDimArray, As::AbstractDimArray...)
_cat((catdim,), A1, As...)
end
function _cat(catdims::Tuple, A1::AbstractDimArray, As::AbstractDimArray...)
Xin = (A1, As...)
newcatdims = map(catdims) do catdim
# If catdim is already constructed, its the new dimension
if catdim isa Dimension
return catdim
end
# Otherwise build a new dimension/lookup
if catdim isa Int
if hasdim(A1, catdim)
catdim = basedims(dims(A1, catdim))
else
return AnonDim(NoLookup()) # TODO: handle larger dimension extensions, this is half broken
end
else
catdim = basedims(name2dim(catdim))
end
# Dimension Types and Symbols
if all(x -> hasdim(x, catdim), Xin)
# We concatenate an existing dimension
newcatdim = if lookup(A1, catdim) isa NoLookup
rebuild(catdim, NoLookup())
else
# vcat the index for the catdim in each of Xin
joindims = map(A -> dims(A, catdim), Xin)
if !check_cat_lookups(joindims...)
return rebuild(catdim, NoLookup())
end
_vcat_dims(joindims...)
end
else
# Concatenate new dims
if all(map(x -> hasdim(refdims(x), catdim), Xin))
if catdim isa Dimension && val(catdim) isa AbstractArray && !(lookup(catdim) isa NoLookup{AutoValues})
# Combine the refdims properties with the passed in catdim
set(refdims(first(Xin), catdim), catdim)
else
# vcat the refdims
_vcat_dims(map(x -> refdims(x, catdim), Xin)...)
end
else
# Use the catdim as the new dimension
catdim
end
end
end
inserted_dims = dims(newcatdims, dims(A1))
appended_dims = otherdims(newcatdims, inserted_dims)
inserted_dnums = dimnum(A1, inserted_dims)
appended_dnums = ntuple(i -> i + length(dims(A1)), length(appended_dims))
cat_dnums = (inserted_dnums..., appended_dnums...)
# Warn if dims or val do not match, and cat the parent
if !comparedims(map(x -> otherdims(x, newcatdims), Xin)...;
order=true, val=true, msg=Dimensions.Warn(" Can't `cat` AbstractDimArray, applying to `parent` object.")
)
return Base.cat(map(parent, Xin)...; dims=cat_dnums)
end
updated_dims = setdims(dims(A1), inserted_dims)
newdims = (updated_dims..., appended_dims...)
newrefdims = otherdims(refdims(A1), newcatdims)
newA = Base.cat(map(parent, Xin)...; dims=cat_dnums)
return rebuild(A1, newA, format(newdims, newA), newrefdims)
end
function Base.hcat(As::Union{AbstractDimVector,AbstractDimMatrix}...)
Base.cat(As; dims=2)
A1 = first(As)
catdim = if A1 isa AbstractDimVector
AnonDim(NoLookup())
else
joindims = map(last ∘ dims, As)
check_cat_lookups(joindims...) || return Base.hcat(map(parent, As)...)
_vcat_dims(joindims...)
end
noncatdim = dims(A1, 1)
# Make sure this is the same dimension for all arrays
if !comparedims(map(x -> dims(x, 1), As)...;
val=true, msg=Dimensions.Warn(" Can't `hcat` AbstractDimArray, applying to `parent` object.")
)
return Base.hcat(map(parent, As)...)
end
newdims = (noncatdim, catdim)
newA = hcat(map(parent, As)...)
return rebuild(A1, newA, format(newdims, newA))
end
function Base.vcat(As::Union{AbstractDimVector,AbstractDimMatrix}...)
A1 = first(As)
firstdims = map(first ∘ dims, As)
check_cat_lookups(firstdims...) || return Base.vcat(map(parent, As)...)
newdims = if A1 isa AbstractDimVector
catdim = _vcat_dims(firstdims...)
(catdim,)
else
# Make sure this is the same dimension for all arrays
if !comparedims(map(x -> dims(x, 2), As)...;
val=true, msg=Dimensions.Warn(" Can't `vcat` AbstractDimArray, applying to `parent` object.")
)
return Base.vcat(map(parent, As)...)
end
catdim = _vcat_dims(firstdims...)
noncatdim = dims(A1, 2)
(catdim, noncatdim)
end
newA = vcat(map(parent, As)...)
return rebuild(A1, newA, format(newdims, newA))
end
function Base.vcat(d1::Dimension, ds::Dimension...)
dims = (d1, ds...)
comparedims(dims...; length=false)
check_cat_lookups(dims...) || return Base.vcat(map(parent, dims)...)
return _vcat_dims(d1, ds...)
end
check_cat_lookups(dims::Dimension...) =
_check_cat_lookups(basetypeof(first(dims)), lookup(dims)...)
# Lookups may need adjustment for `cat`
_check_cat_lookups(D, lookups::Lookup...) = _check_cat_lookup_order(D, lookups...)
_check_cat_lookups(D, l1::NoLookup, lookups::NoLookup...) = true
function _check_cat_lookups(D, l1::AbstractSampled, lookups::AbstractSampled...)
length(lookups) > 0 || return true
_check_cat_lookup_order(D, l1, lookups...) || return false
_check_cat_lookups(D, span(l1), l1, lookups...)
end
function _check_cat_lookups(D, ::Regular, lookups...)
length(lookups) > 1 || return true
lastval = last(first(lookups))
s = step(first(lookups))
map(Base.tail(lookups)) do l
if !(span(l) isa Regular)
_mixed_span_warn(D, Regular, span(l))
return false
end
if !(step(span(l)) == s)
@warn _cat_warn_string(D, "step sizes $(step(span(l))) and $s do not match")
return false
end
if !(lastval + s ≈ first(l))
@warn _cat_warn_string(D, "`Regular` lookups do not join with the correct step size: $(lastval) + $s ≈ $(first(l)) should hold")
return false
end
lastval = last(l)
return true
end |> all
end
function _check_cat_lookups(D, ::Explicit, lookups...)
map(lookups) do l
span(l) isa Explicit || _mixed_span_warn(D, Explicit, span(l))
end |> all
end
function _check_cat_lookups(D, ::Irregular, lookups...)
map(lookups) do l
span(l) isa Irregular || _mixed_span_warn(D, Irregular, span(l))
end |> all
end
function _check_cat_lookup_order(D, lookups::Lookup...)
length(lookups) > 1 || return true
l1 = first(lookups)
length(l1) == 0 && return _check_cat_lookup_order(D, Base.tail(lookups)...)
L = basetypeof(l1)
x = last(l1)
if isordered(l1)
map(Base.tail(lookups)) do lookup
length(lookup) > 0 || return true
if isforward(lookup)
if isreverse(l1)
_cat_mixed_ordered_warn(D)
return false
elseif length(lookup) == 0 || first(lookup) > x
x = last(lookup)
return true
else
x = last(lookup)
_cat_lookup_overlap_warn(D, first(lookup), x)
return false
end
else
if isforward(l1)
_cat_mixed_ordered_warn(D)
return false
elseif length(lookup) == 0 || first(lookup) < x
x = last(lookup)
return true
else
x = last(lookup)
_cat_lookup_overlap_warn(D, first(lookup), x)
return false
end
end
end |> all
else
intr = intersect(lookups...)
if length(intr) == 0
return true
else
_cat_lookup_intersect_warn(D, intr)
return false
end
end
end
function _vcat_dims(d1::Dimension, ds::Dimension...)
dims = (d1, ds...)
newlookup = _vcat_lookups(lookup(dims)...)
return rebuild(d1, newlookup)
end
# Lookups may need adjustment for `cat`
function _vcat_lookups(lookups::Lookup...)
newindex = _vcat_index(lookups...)
return rebuild(lookups[1]; data=newindex)
end
function _vcat_lookups(lookups::AbstractSampled...)
newindex = _vcat_index(lookups...)
newlookup = _vcat_lookups(sampling(first(lookups)), span(first(lookups)), lookups...)
return rebuild(newlookup; data=newindex)
end
function _vcat_lookups(::Any, ::Regular, lookups...)
first(lookups)
end
function _vcat_lookups(::Intervals, ::Explicit, lookups...)
len = mapreduce(+, lookups) do l
size(val(span(l)), 2)
end
combined_span_mat = similar(val(span(first(lookups))), 2, len)
i = 1
foreach(lookups) do l
span_mat = val(span(l))
l = size(span_mat, 2)
combined_span_mat[:, i:i+l - 1] .= span_mat
i += l
end
rebuild(first(lookups); span=Explicit(combined_span_mat))
end
function _vcat_lookups(::Intervals, ::Irregular, lookups...)
allbounds = map(bounds ∘ span, lookups)
newbounds = minimum(map(first, allbounds)), maximum(map(last, allbounds))
rebuild(lookups[1]; span=Irregular(newbounds))
end
function _vcat_lookups(::Points, ::Irregular, lookups...)
rebuild(first(lookups); span=Irregular(nothing, nothing))
end
_vcat_index(A1::NoLookup, A::NoLookup...) = OneTo(mapreduce(length, +, (A1, A...)))
# TODO: handle vcat OffsetArrays?
# Otherwise just vcat. TODO: handle order breaking vcat?
# function _vcat_index(lookup::Lookup, lookups...)
# _vcat_index(span(lookup), lookup, lookups...)
# end
function _vcat_index(lookup1::Lookup, lookups::Lookup...)
shifted = map((lookup1, lookups...)) do l
parent(maybeshiftlocus(locus(lookup1), l))
end
return reduce(vcat, shifted)
end
@noinline _cat_mixed_ordered_warn(D) = @warn _cat_warn_string(D, "`Ordered` lookups are mixed `ForwardOrdered` and `ReverseOrdered`")
@noinline _cat_lookup_overlap_warn(D, x1, x2) = @warn _cat_warn_string(D, "`Ordered` lookups are misaligned at $x2 and $x1")
@noinline _cat_lookup_intersect_warn(D, intr) = @warn _cat_warn_string(D, "`Unorderd` lookups share values: $intr")
@noinline _mixed_span_error(D, S, span) = throw(DimensionMismatch(_span_string(D, S, span)))
@noinline function _mixed_span_warn(D, S, span)
@warn _span_string(D, S, span)
return false
end
_span_string(D, S, span) = _cat_warn_string(D, "not all lookups have `$S` spans. Found $(basetypeof(span))")
_cat_warn_string(D, message) = """
`cat` cannot concatenate `Dimension`s, falling back to `parent` type:
$message on dimension $D.
To fix for `AbstractDimArray`, pass new lookup values as `cat(As...; dims=$D(newlookupvals))` keyword or `dims=$D()` for empty `NoLookup`.
"""
function Base.inv(A::AbstractDimArray{T,2}) where T
newdata = inv(parent(A))
newdims = reverse(dims(A))
rebuild(A, newdata, newdims)
end
# Index breaking
# TODO: change the index and traits of the reduced dimension and return a DimArray.
Base.unique(A::AbstractDimArray; dims::Union{DimOrDimType,Int,Colon}=:) = _unique(A, dims)
Base.unique(A::AbstractDimArray{<:Any,1}) = unique(parent(A))
_unique(A::AbstractDimArray, dims) = unique(parent(A); dims=dimnum(A, dims))
_unique(A::AbstractDimArray, dims::Colon) = unique(parent(A); dims=:)
Base.diff(A::AbstractDimVector; dims=1) = _diff(A, dimnum(A, dims))
Base.diff(A::AbstractDimArray; dims) = begin
_diff(A, dimnum(A, dims))
end
@inline function _diff(A::AbstractDimArray{<:Any,N}, dims::Integer) where {N}
r = axes(A)
# Copied from Base.diff
r0 = ntuple(i -> i == dims ? UnitRange(1, last(r[i]) - 1) : UnitRange(r[i]), N)
rebuildsliced(A, diff(parent(A); dims=dimnum(A, dims)), r0)
end
# Forward `replace` to parent objects
function Base._replace!(new::Base.Callable, res::AbstractDimArray, A::AbstractDimArray, count::Int)
Base._replace!(new, parent(res), parent(A), count)
return res
end
Base.reverse(A::AbstractDimArray; dims=:) = _reverse(A, dims)
function _reverse(A::AbstractDimArray, ::Colon)
newdims = _reverse(DD.dims(A))
newdata = reverse(parent(A))
# Use setdims here because newdims is not all the dims
setdims(rebuild(A, newdata), newdims)
end
function _reverse(A::AbstractDimArray, dims)
newdims = _reverse(DD.dims(A, dims))
newdata = reverse(parent(A); dims=dimnum(A, dims))
# Use setdims here because newdims is not all the dims
setdims(rebuild(A, newdata), newdims)
end
_reverse(dims::Tuple{Vararg{Dimension}}) = map(d -> reverse(d), dims)
_reverse(dim::Dimension) = reverse(dim)
# Dimension
Base.reverse(dim::Dimension) = rebuild(dim, reverse(lookup(dim)))
Base.dataids(A::AbstractDimArray) = Base.dataids(parent(A))
# We need to override copy_similar because our `similar` doesn't work with size changes
# Fixed in Base in https://github.com/JuliaLang/julia/pull/53210
LinearAlgebra.copy_similar(A::AbstractDimArray, ::Type{T}) where {T} = copyto!(similar(A, T), A)