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WIP: introduce DeleteVector #53

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e9b7d35
introduce DeleteVector as workaround of JuliaLang/julia#24909
ranocha Oct 14, 2021
4c401b6
use DeleteVectors for the edge sets of the PartitionIterator
ranocha Oct 14, 2021
bcea53b
fix deleteat with ranges
ranocha Oct 14, 2021
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98 changes: 98 additions & 0 deletions src/DeleteVectors.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
module DeleteVectors

export DeleteVector

# mutable struct DeleteVector{T, Parent <: AbstractVector{T}} <: AbstractVector{T}
# parent::Parent
# length::Int
# end

struct DeleteVector{T, Parent <: AbstractVector{T}} <: AbstractVector{T}
parent::Parent
length::Base.RefValue{Int}
end


function DeleteVector(parent::AbstractVector)
DeleteVector(parent, Ref(length(parent)))
end

function DeleteVector{T}(sizehint::Integer = 4) where {T}
sizehint >= 0 || throw(DomainError(sizehint, "Invalid initial size."))
DeleteVector(Vector{T}(undef, sizehint), Ref(0))
end

@inline Base.parent(v::DeleteVector) = v.parent
@inline Base.pointer(v::DeleteVector) = pointer(parent(v))
@inline Base.pointer(v::DeleteVector, i::Integer) = pointer(parent(v), i)

@inline Base.size(v::DeleteVector) = (v.length[], )
Base.IndexStyle(::DeleteVector) = IndexLinear()

@inline function Base.getindex(v::DeleteVector, i)
@boundscheck checkbounds(v, i)
@inbounds v.parent[i]
end

@inline function Base.setindex!(v::DeleteVector, x, i)
@boundscheck checkbounds(v, i)
@inbounds v.parent[i] = x
end


Base.copy(v::DeleteVector) = DeleteVector(copy(parent(v)), Ref(length(v)))
Base.similar(v::DeleteVector) = DeleteVector(similar(parent(v)), Ref(length(v)))

function Base.copyto!(dest::DeleteVector, doffs::Integer,
src::DeleteVector, soffs::Integer, n::Integer)
copyto!(parent(dest), doffs, parent(src), soffs, n)
end

Base.view(v::DeleteVector, inds::UnitRange) = view(parent(v), inds)


function Base.sizehint!(v::DeleteVector, n)
if length(parent(v)) < n || n >= length(v)
resize!(v.parent, n)
end
nothing
end

function Base.resize!(v::DeleteVector, n)
if length(parent(v)) < n
resize!(v.parent, n)
end
v.length[] = n
v
end

Base.empty!(v::DeleteVector) = (v.length[] = 0; v)


function Base.deleteat!(v::DeleteVector, i::Integer)
@boundscheck checkbounds(v, i)
p = parent(v)
for j in i+1:lastindex(v)
@inbounds p[j-1] = p[j]
end
v.length[] -= 1
v
end

function Base.deleteat!(v::DeleteVector, inds::UnitRange)
@boundscheck checkbounds(v, inds)
p = parent(v)
i = first(inds)
offset = length(inds)
for j in i+offset:lastindex(v)
@inbounds p[j-offset] = p[j]
end
v.length[] -= offset
v
end


Base.findprev(v::DeleteVector, i::Integer) = findprev(parent(v), i)
# TODO: findnext, findlast, findfirst, function arguments

end # module
42 changes: 26 additions & 16 deletions src/RootedTrees.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ using Latexify: Latexify
using RecipesBase: RecipesBase


include("DeleteVectors.jl")
using .DeleteVectors


export RootedTree, rootedtree, rootedtree!, RootedTreeIterator

export butcher_representation
Expand Down Expand Up @@ -369,7 +373,11 @@ end
const BUFFER_LENGTH = 64
const CANONICAL_REPRESENTATION_BUFFER = Vector{Vector{Int}}()

function canonical_representation!(t::RootedTree{Int, Vector{Int}})
function canonical_representation!(t::Union{
RootedTree{Int, Vector{Int}},
RootedTree{Int, DeleteVector{Int, Vector{Int}}},
RootedTree{Int, SubArray{Int, 1, Vector{Int}, Tuple{UnitRange{Int}}, true}},
RootedTree{Int, SubArray{Int, 1, Vector{Int}, Tuple{Base.OneTo{Int}}, true}}})
if order(t) <= BUFFER_LENGTH
buffer = CANONICAL_REPRESENTATION_BUFFER[Threads.threadid()]
else
Expand Down Expand Up @@ -616,10 +624,10 @@ Section 2.3 of
Foundations of Computational Mathematics
[DOI: 10.1007/s10208-010-9065-1](https://doi.org/10.1007/s10208-010-9065-1)
"""
struct PartitionForestIterator{T, V, Tree<:RootedTree{T, V}}
struct PartitionForestIterator{T, V, Tree<:RootedTree{T, V}, EdgeSet<:AbstractVector{Bool}}
t::Tree
level_sequence::V
edge_set::Vector{Bool}
edge_set::EdgeSet
end

function PartitionForestIterator(t::RootedTree, edge_set)
Expand Down Expand Up @@ -713,8 +721,8 @@ function partition_skeleton(t::RootedTree, edge_set)
end

edge_set_copy = copy(edge_set)
skeleton = RootedTree(copy(t.level_sequence), true)
return partition_skeleton!(skeleton.level_sequence, edge_set_copy)
level_sequence_copy = copy(t.level_sequence)
return partition_skeleton!(level_sequence_copy, edge_set_copy)
end

# internal in-place version of partition_skeleton modifying the inputs
Expand All @@ -730,7 +738,8 @@ function partition_skeleton!(level_sequence, edge_set)
# Remember the convention node = edge + 1
subtree_root_index = edge_to_contract + 1
subtree_last_index = subtree_root_index + 1
while subtree_last_index <= length(level_sequence)
length_level_sequence = length(level_sequence)
while subtree_last_index <= length_level_sequence
if level_sequence[subtree_last_index] > level_sequence[subtree_root_index]
level_sequence[subtree_last_index] -= 1
subtree_last_index += 1
Expand Down Expand Up @@ -787,7 +796,7 @@ end
# A helper function to comute the binary representation of an integer `n` as
# a vector of `Bool`s. This is a more efficient version of
# binary_digits!(digits, n) = digits!(digits, n, base=2)
function binary_digits!(digits::Vector{Bool}, n::Int)
function binary_digits!(digits::AbstractVector{Bool}, n::Int)
bit = 1
for i in eachindex(digits)
digits[i] = n & bit > 0
Expand Down Expand Up @@ -819,23 +828,24 @@ Section 2.3 of
Foundations of Computational Mathematics
[DOI: 10.1007/s10208-010-9065-1](https://doi.org/10.1007/s10208-010-9065-1)
"""
struct PartitionIterator{T, Tree<:RootedTree{T}}
struct PartitionIterator{T, Tree<:RootedTree{T}, EdgeSet<:AbstractVector{Bool}}
t::Tree
forest::PartitionForestIterator{T, Vector{T}, RootedTree{T, Vector{T}}}
skeleton::RootedTree{T, Vector{T}}
edge_set::Vector{Bool}
edge_set_tmp::Vector{Bool}
edge_set::EdgeSet
edge_set_tmp::EdgeSet
end

function PartitionIterator(t::Tree) where {T, Tree<:RootedTree{T}}
skeleton = RootedTree(Vector{T}(undef, order(t)), true)
edge_set = Vector{Bool}(undef, order(t) - 1)
edge_set = DeleteVector(Vector{Bool}(undef, order(t) - 1))
edge_set_tmp = similar(edge_set)

t_forest = RootedTree(Vector{T}(undef, order(t)), true)
level_sequence = similar(t_forest.level_sequence)
forest = PartitionForestIterator(t_forest, level_sequence, edge_set_tmp)
PartitionIterator{T, Tree}(t, forest, skeleton, edge_set, edge_set_tmp)
PartitionIterator{T, Tree, typeof(edge_set)}(
t, forest, skeleton, edge_set, edge_set_tmp)
end

# Allocate global buffer for `PartitionIterator` for each thread
Expand All @@ -857,22 +867,22 @@ function PartitionIterator(t::RootedTree{Int, Vector{Int}})
resize!(level_sequence, order_t)
buffer_skeleton = PARTITION_ITERATOR_BUFFER_SKELETON[id]
resize!(buffer_skeleton, order_t)
edge_set = PARTITION_ITERATOR_BUFFER_EDGE_SET[id]
edge_set = PARTITION_ITERATOR_BUFFER_EDGE_SET[id] |> DeleteVector
resize!(edge_set, order_t - 1)
edge_set_tmp = PARTITION_ITERATOR_BUFFER_EDGE_SET_TMP[id]
edge_set_tmp = PARTITION_ITERATOR_BUFFER_EDGE_SET_TMP[id] |> DeleteVector
resize!(edge_set_tmp, order_t - 1)
else
buffer_forest_t = Vector{Int}(undef, order_t)
level_sequence = similar(buffer_forest_t)
buffer_skeleton = similar(buffer_forest_t)
edge_set = Vector{Bool}(undef, order_t - 1)
edge_set = Vector{Bool}(undef, order_t - 1) |> DeleteVector
edge_set_tmp = similar(edge_set)
end

skeleton = RootedTree(buffer_skeleton, true)
t_forest = RootedTree(buffer_forest_t, true)
forest = PartitionForestIterator(t_forest, level_sequence, edge_set_tmp)
PartitionIterator{Int, RootedTree{Int, Vector{Int}}}(
PartitionIterator{Int, RootedTree{Int, Vector{Int}}, typeof(edge_set)}(
t, forest, skeleton, edge_set, edge_set_tmp)
end

Expand Down