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Merged
merged 3 commits into from
Apr 10, 2023
Merged

safer inbounds in RaggedMatrix #431

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8fe2766
safer inbounds in RaggedMatrix
jishnub Apr 10, 2023
6fe262d
fix RaggedMatrix constructor colstop checks
jishnub Apr 10, 2023
0ea13cb
propagate_inbounds in get and setindex
jishnub Apr 10, 2023
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90 changes: 47 additions & 43 deletions src/LinearAlgebra/RaggedMatrix.jl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# FiniteRange gives the nonzero entries in a row/column
struct FiniteRange end

getindex(A::AbstractMatrix,::Type{FiniteRange},j::Integer) = A[1:colstop(A,j),j]
getindex(A::AbstractMatrix,::Type{FiniteRange},j::Integer) = A[colrange(A,j),j]
getindex(A::AbstractMatrix,k::Integer,::Type{FiniteRange}) = A[k,1:rowstop(A,k)]

const ⤓ = FiniteRange
Expand Down Expand Up @@ -32,40 +32,48 @@ RaggedMatrix{T}(::UndefInitializer, m::Int, colns::AbstractVector{Int}) where {T
RaggedMatrix(Vector{T}(undef, sum(colns)),Int[1;1 .+ cumsum(colns)],m)


Base.size(A::RaggedMatrix) = (A.m,length(A.cols)-1)
size(A::RaggedMatrix) = (A.m,length(A.cols)-1)

colstart(A::RaggedMatrix,j::Integer) = 1
colstop(A::RaggedMatrix,j::Integer) = min(A.cols[j+1]-A.cols[j],size(A,1))

@inline function incol(A, k, j, ind = A.cols[j]+k-1)
Base.@propagate_inbounds function incol(A, k, j, ind = A.cols[j]+k-1)
ind < A.cols[j+1]
end

function getindex(A::RaggedMatrix,k::Int,j::Int)
if k>size(A,1) || k < 1 || j>size(A,2) || j < 1
Base.@propagate_inbounds function incols_getindex(A::RaggedMatrix, k::Int, j::Int, ind = A.cols[j]+k-1)
A.data[ind]
end
Base.@propagate_inbounds function incols_setindex!(A::RaggedMatrix, v, k::Int, j::Int, ind = A.cols[j]+k-1)
A.data[ind] = v
A
end

Base.@propagate_inbounds function getindex(A::RaggedMatrix,k::Int,j::Int)
@boundscheck if k>size(A,1) || k < 1 || j>size(A,2) || j < 1
throw(BoundsError(A,(k,j)))
end

ind = A.cols[j]+k-1
if incol(A, k, j, ind)
A.data[ind]
incols_getindex(A, k, j, ind)
else
zero(eltype(A))
end
end

function Base.setindex!(A::RaggedMatrix,v,k::Int,j::Int)
if k>size(A,1) || k < 1 || j>size(A,2) || j < 1
Base.@propagate_inbounds function setindex!(A::RaggedMatrix,v,k::Int,j::Int)
@boundscheck if k>size(A,1) || k < 1 || j>size(A,2) || j < 1
throw(BoundsError(A,(k,j)))
end

ind = A.cols[j]+k-1
if incol(A, k, j, ind)
A.data[ind]=v
incols_setindex!(A, v, k, j, ind)
elseif v ≠ 0
throw(BoundsError(A,(k,j)))
throw(ArgumentError("Can't set index $((k,j)) of a RaggedMatrix to a non-zero value"))
end
v
A
end

convert(::Type{RaggedMatrix{T}}, R::RaggedMatrix{T}) where T = R
Expand All @@ -75,40 +83,32 @@ convert(::Type{RaggedMatrix{T}}, R::RaggedMatrix) where T =


function convert(::Type{Matrix{T}}, A::RaggedMatrix) where T
ret = zeros(T,size(A,1),size(A,2))
for j=1:size(A,2)
ret[1:colstop(A,j),j] = view(A,1:colstop(A,j),j)
ret = zeros(T, size(A))
@inbounds for j in axes(A,2), k in colrange(A,j)
v = incols_getindex(A, k, j)
ret[k,j] = v
end
ret
end

convert(::Type{Matrix}, A::RaggedMatrix) = Matrix{eltype(A)}(A)

function convert(::Type{RaggedMatrix{T}}, B::BandedMatrix) where T
l = bandwidth(B,1)
ret = RaggedMatrix(Zeros{T}(size(B)), Int[colstop(B,j) for j=1:size(B,2)])
for j=1:size(B,2),k=colrange(B,j)
ret[k,j] = B[k,j]
end
ret
end

convert(::Type{RaggedMatrix}, B::BandedMatrix) = RaggedMatrix{eltype(B)}(B)

function convert(::Type{RaggedMatrix{T}}, B::AbstractMatrix) where T
ret = RaggedMatrix(Zeros{T}(size(B)), Int[colstop(B,j) for j=1:size(B,2)])
for j=1:size(B,2), k=colrange(B,j)
ret[k,j] = B[k,j]
ret = RaggedMatrix(Zeros{T}(size(B)), Int[colstop(B,j) for j=axes(B,2)])
@inbounds for j in axes(B,2), k in colrange(B,j)
incols_setindex!(ret, B[k,j], k, j)
end
ret
end

convert(::Type{RaggedMatrix}, B::AbstractMatrix) = RaggedMatrix{eltype(B)}(B)
convert(::Type{RaggedMatrix}, B::AbstractMatrix) = strictconvert(RaggedMatrix{eltype(B)}, B)

RaggedMatrix(B::AbstractMatrix) = strictconvert(RaggedMatrix, B)
RaggedMatrix{T}(B::AbstractMatrix) where T = strictconvert(RaggedMatrix{T}, B)

Base.similar(B::RaggedMatrix,::Type{T}) where {T} = RaggedMatrix(similar(B.data, T),copy(B.cols),B.m)
similar(B::RaggedMatrix,::Type{T}) where {T} = RaggedMatrix(similar(B.data, T),copy(B.cols),B.m)

for (op,bop) in ((:(Base.rand), :rrand),)
@eval begin
Expand All @@ -126,9 +126,13 @@ function RaggedMatrix{T}(Z::Zeros, colns::AbstractVector{Int}) where {T}
end

function RaggedMatrix{T}(A::AbstractMatrix, colns::AbstractVector{Int}) where T
Base.require_one_based_indexing(A)
Base.require_one_based_indexing(colns)
ret = RaggedMatrix{T}(undef, size(A,1), colns)
@inbounds for j = 1:length(colns), k = 1:colns[j]
ret[k,j] = A[k,j]
(length(colns) == size(A,2) && all(<=(size(A,1)), colns)) ||
throw(ArgumentError("column stops $colns incompatible with input matrix of size $(size(A))"))
for j in axes(A,2), k = 1:colns[j]
@inbounds incols_setindex!(ret, A[k,j], k, j)
end
ret
end
Expand All @@ -149,7 +153,7 @@ function mul!(y::Vector, A::RaggedMatrix, b::Vector)
end
T=eltype(y)
fill!(y,zero(T))
for j=1:m
for j in axes(A,2)
kr=A.cols[j]:A.cols[j+1]-1
axpy!(b[j],view(A.data,kr),view(y,1:length(kr)))
end
Expand All @@ -165,7 +169,7 @@ function axpy!(a, X::RaggedMatrix, Y::RaggedMatrix)
if X.cols == Y.cols
axpy!(a,X.data,Y.data)
else
for j = 1:size(X,2)
for j = axes(X,2)
Xn = colstop(X,j)
Yn = colstop(Y,j)
if Xn > Yn # check zeros otherwise
Expand All @@ -174,8 +178,8 @@ function axpy!(a, X::RaggedMatrix, Y::RaggedMatrix)
end
end
cs = min(Xn,Yn)
axpy!(a,view(X.data,X.cols[j]:X.cols[j]+cs-1),
view(Y.data,Y.cols[j]:Y.cols[j]+cs-1))
axpy!(a, view(X.data, range(X.cols[j], length=cs)),
view(Y.data, range(Y.cols[j], length=cs)))
end
end
Y
Expand All @@ -196,7 +200,7 @@ function axpy!(a,X::RaggedMatrix,
ksh = first(parentindices(Y)[1]) - 1 # how much to shift
jsh = first(parentindices(Y)[2]) - 1 # how much to shift

for j=1:size(X,2)
for j=axes(X,2)
cx=colstop(X,j)
cy=colstop(Y,j)
if cx > cy
Expand All @@ -205,7 +209,7 @@ function axpy!(a,X::RaggedMatrix,
throw(BoundsError("Trying to add a non-zero to a zero."))
end
end
kr = X.cols[j]:X.cols[j]+cy-1
kr = range(X.cols[j], length=cy)
else
kr = X.cols[j]:X.cols[j+1]-1
end
Expand All @@ -222,7 +226,7 @@ end
function *(A::RaggedMatrix,B::RaggedMatrix)
cols = zeros(Int,size(B,2))
T = promote_type(eltype(A),eltype(B))
for j=1:size(B,2),k=1:colstop(B,j)
for j=axes(B,2),k=colrange(B,j)
cols[j] = max(cols[j],colstop(A,k))
end

Expand All @@ -232,23 +236,23 @@ end
function unsafe_mul!(Y::RaggedMatrix,A::RaggedMatrix,B::RaggedMatrix)
fill!(Y.data,0)

for j=1:size(B,2),k=1:colstop(B,j)
axpy!(B[k,j], view(A,1:colstop(A,k),k),
view(Y.data,Y.cols[j] .- 1 .+ (1:colstop(A,k))))
for j=axes(B,2),k=colrange(B,j)
axpy!(B[k,j], view(A,colrange(A,k),k),
view(Y.data,Y.cols[j] .- 1 .+ (colrange(A,k))))
end

Y
end

function mul!(Y::RaggedMatrix,A::RaggedMatrix,B::RaggedMatrix)
for j=1:size(B,2)
for j=axes(B,2)
col = 0
for k=1:colstop(B,j)
for k=colrange(B,j)
col = max(col,colstop(A,k))
end

if col > colstop(Y,j)
throw(BoundsError())
throw(BoundsError(Y, (col,j)))
end
end

Expand Down