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Replace the LGPL-licensed sparse() parent method with an MIT-licensed…
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… version. See #13001 and #14631.
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@Sacha0
Sacha0 committed Jan 27, 2016
1 parent df928bd commit 6fa8436
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124 changes: 0 additions & 124 deletions base/sparse/csparse.jl
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Expand Up @@ -13,130 +13,6 @@
# Section 2.4: Triplet form
# http:https://www.cise.ufl.edu/research/sparse/CSparse/

"""
sparse(I,J,V,[m,n,combine])
Create a sparse matrix `S` of dimensions `m x n` such that `S[I[k], J[k]] = V[k]`.
The `combine` function is used to combine duplicates. If `m` and `n` are not
specified, they are set to `maximum(I)` and `maximum(J)` respectively. If the
`combine` function is not supplied, duplicates are added by default. All elements
of `I` must satisfy `1 <= I[k] <= m`, and all elements of `J` must satisfy `1 <= J[k] <= n`.
"""
function sparse{Tv,Ti<:Integer}(I::AbstractVector{Ti},
J::AbstractVector{Ti},
V::AbstractVector{Tv},
nrow::Integer, ncol::Integer,
combine::Union{Function,Base.Func})

N = length(I)
if N != length(J) || N != length(V)
throw(ArgumentError("triplet I,J,V vectors must be the same length"))
end
if N == 0
return spzeros(eltype(V), Ti, nrow, ncol)
end

# Work array
Wj = Array(Ti, max(nrow,ncol)+1)

# Allocate sparse matrix data structure
# Count entries in each row
Rnz = zeros(Ti, nrow+1)
Rnz[1] = 1
nz = 0
for k=1:N
iind = I[k]
iind > 0 || throw(ArgumentError("all I index values must be > 0"))
iind <= nrow || throw(ArgumentError("all I index values must be ≤ the number of rows"))
if V[k] != 0
Rnz[iind+1] += 1
nz += 1
end
end
Rp = cumsum(Rnz)
Ri = Array(Ti, nz)
Rx = Array(Tv, nz)

# Construct row form
# place triplet (i,j,x) in column i of R
# Use work array for temporary row pointers
@simd for i=1:nrow; @inbounds Wj[i] = Rp[i]; end

@inbounds for k=1:N
iind = I[k]
jind = J[k]
jind > 0 || throw(ArgumentError("all J index values must be > 0"))
jind <= ncol || throw(ArgumentError("all J index values must be ≤ the number of columns"))
p = Wj[iind]
Vk = V[k]
if Vk != 0
Wj[iind] += 1
Rx[p] = Vk
Ri[p] = jind
end
end

# Reset work array for use in counting duplicates
@simd for j=1:ncol; @inbounds Wj[j] = 0; end

# Sum up duplicates and squeeze
anz = 0
@inbounds for i=1:nrow
p1 = Rp[i]
p2 = Rp[i+1] - 1
pdest = p1

for p = p1:p2
j = Ri[p]
pj = Wj[j]
if pj >= p1
Rx[pj] = combine(Rx[pj], Rx[p])
else
Wj[j] = pdest
if pdest != p
Ri[pdest] = j
Rx[pdest] = Rx[p]
end
pdest += one(Ti)
end
end

Rnz[i] = pdest - p1
anz += (pdest - p1)
end

# Transpose from row format to get the CSC format
RiT = Array(Ti, anz)
RxT = Array(Tv, anz)

# Reset work array to build the final colptr
Wj[1] = 1
@simd for i=2:(ncol+1); @inbounds Wj[i] = 0; end
@inbounds for j = 1:nrow
p1 = Rp[j]
p2 = p1 + Rnz[j] - 1
for p = p1:p2
Wj[Ri[p]+1] += 1
end
end
RpT = cumsum(Wj[1:(ncol+1)])

# Transpose
@simd for i=1:length(RpT); @inbounds Wj[i] = RpT[i]; end
@inbounds for j = 1:nrow
p1 = Rp[j]
p2 = p1 + Rnz[j] - 1
for p = p1:p2
ind = Ri[p]
q = Wj[ind]
Wj[ind] += 1
RiT[q] = j
RxT[q] = Rx[p]
end
end

return SparseMatrixCSC(nrow, ncol, RpT, RiT, RxT)
end

# Compute the elimination tree of A using triu(A) returning the parent vector.
# A root node is indicated by 0. This tree may actually be a forest in that
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214 changes: 213 additions & 1 deletion base/sparse/sparsematrix.jl
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Expand Up @@ -318,7 +318,219 @@ function sparse_IJ_sorted!{Ti<:Integer}(I::AbstractVector{Ti}, J::AbstractVector
return SparseMatrixCSC(m, n, colptr, I, V)
end

## sparse() can take its inputs in unsorted order (the parent method is now in csparse.jl)
"""
sparse(I, J, V, [m, n, combine])
Create a sparse matrix `S` of dimensions `m` x `n` such that `S[I[k], J[k]] = V[k]`. The
`combine` function is used to combine duplicates. If `m` and `n` are not specified, they
are set to `maximum(I)` and `maximum(J)` respectively. If the `combine` function is not
supplied, duplicates are added by default. All elements of `I` must satisfy
`1 <= I[k] <= m`, and all elements of `J` must satisfy `1 <= J[k] <= n`.
For additional documentation and an expert driver, see `Base.SparseArrays.sparse!`.
"""
function sparse{Tv,Ti<:Integer}(I::AbstractVector{Ti}, J::AbstractVector{Ti}, V::AbstractVector{Tv}, m::Integer, n::Integer, combine)
coolen = length(I)
if length(J) != coolen || length(V) != coolen
throw(ArgumentError(string("the first three arguments' lengths must match, ",
"length(I) (=$(length(I))) == length(J) (= $(length(J))) == length(V) (= ",
"$(length(V)))")))
end

if m == 0 || n == 0 || coolen == 0
if coolen != 0
if n == 0
throw(ArgumentError("column indices J[k] must satisfy 1 <= J[k] <= n"))
elseif m == 0
throw(ArgumentError("row indices I[k] must satisfy 1 <= I[k] <= m"))
end
end
SparseMatrixCSC(m, n, ones(Ti, n+1), Vector{Ti}(), Vector{Tv}())
else
# Allocate storage for CSR form
csrrowptr = Vector{Ti}(m+1)
csrcolval = Vector{Ti}(coolen)
csrnzval = Vector{Tv}(coolen)

# Allocate storage for the CSC form's column pointers and a necessary workspace
csccolptr = Vector{Ti}(n+1)
klasttouch = Vector{Ti}(n)

# Allocate empty arrays for the CSC form's row and nonzero value arrays
# The parent method called below automagically resizes these arrays
cscrowval = Vector{Ti}()
cscnzval = Vector{Tv}()

sparse!(I, J, V, m, n, combine, klasttouch,
csrrowptr, csrcolval, csrnzval,
csccolptr, cscrowval, cscnzval )
end
end

"""
sparse!{Tv,Ti<:Integer}(
I::AbstractVector{Ti}, J::AbstractVector{Ti}, V::AbstractVector{Tv},
m::Integer, n::Integer, combine, klasttouch::Vector{Ti},
csrrowptr::Vector{Ti}, csrcolval::Vector{Ti}, csrnzval::Vector{Tv},
[csccolptr::Vector{Ti}], [cscrowval::Vector{Ti}, cscnzval::Vector{Tv}] )
Parent of and expert driver for `sparse`; see `sparse` for basic usage. This method
allows the user to provide preallocated storage for `sparse`'s intermediate objects and
result as described below. This capability enables more efficient successive construction
of `SparseMatrixCSC`s from coordinate representations, and also enables extraction of an
unsorted-column representation of the result's transpose at no additional cost.
This method consists of three major steps: (1) Counting-sort the provided coordinate
representation into an unsorted-row CSR form including repeated entries. (2) Sweep through
the CSR form, simultaneously calculating the desired CSC form's column-pointer array,
detecting repeated entries, and repacking the CSR form with repeated entries combined;
this stage yields an unsorted-row CSR form with no repeated entries. (3) Counting-sort the
preceding CSR form into a fully-sorted CSC form with no repeated entries.
Input arrays `csrrowptr`, `csrcolval`, and `csrnzval` constitute storage for the
intermediate CSR forms and require `length(csrrowptr) >= m + 1`,
`length(csrcolval) >= length(I)`, and `length(csrnzval >= length(I))`. Input
array `klasttouch`, workspace for the second stage, requires `length(klasttouch) >= n`.
Optional input arrays `csccolptr`, `cscrowval`, and `cscnzval` constitute storage for the
returned CSC form `S`. `csccolptr` requires `length(csccolptr) >= n + 1`. If necessary,
`cscrowval` and `cscnzval` are automatically resized to satisfy
`length(cscrowval) >= nnz(S)` and `length(cscnzval) >= nnz(S)`; hence, if `nnz(S)` is
unknown at the outset, passing in empty vectors of the appropriate type (`Vector{Ti}()`
and `Vector{Tv}()` respectively) suffices, or calling the `sparse!` method
neglecting `cscrowval` and `cscnzval`.
On return, `csrrowptr`, `csrcolval`, and `csrnzval` contain an unsorted-column
representation of the result's transpose.
For the sake of efficiency, this method performs no argument checking beyond
`1 <= I[k] <= m` and `1 <= J[k] <= n`. Use with care. Testing with `--check-bounds=yes`
is wise.
This method runs in `O(m, n, length(I))` time. The HALFPERM algorithm described in
F. Gustavson, "Two fast algorithms for sparse matrices: multiplication and permuted
transposition," ACM TOMS 4(3), 250-269 (1978) inspired this method's use of a pair of
counting sorts.
Performance note: As of January 2016, `combine` should be a functor for this method to
perform well. This caveat may disappear when the work in `jb/functions` lands.
"""
function sparse!{Tv,Ti<:Integer}(I::AbstractVector{Ti}, J::AbstractVector{Ti},
V::AbstractVector{Tv}, m::Integer, n::Integer, combine, klasttouch::Vector{Ti},
csrrowptr::Vector{Ti}, csrcolval::Vector{Ti}, csrnzval::Vector{Tv},
csccolptr::Vector{Ti}, cscrowval::Vector{Ti}, cscnzval::Vector{Tv} )

# Compute the CSR form's row counts and store them shifted forward by one in csrrowptr
fill!(csrrowptr, 0)
coolen = length(I)
@inbounds for k in 1:coolen
Ik = I[k]
if 1 > Ik || m < Ik
throw(ArgumentError("row indices I[k] must satisfy 1 <= I[k] <= m"))
end
csrrowptr[Ik+1] += 1
end

# Compute the CSR form's rowptrs and store them shifted forward by one in csrrowptr
countsum = 1
csrrowptr[1] = 1
@inbounds for i in 2:(m+1)
overwritten = csrrowptr[i]
csrrowptr[i] = countsum
countsum += overwritten
end

# Counting-sort the column and nonzero values from J and V into csrcolval and csrnzval
# Tracking write positions in csrrowptr corrects the row pointers
@inbounds for k in 1:coolen
Ik, Jk = I[k], J[k]
if 1 > Jk || n < Jk
throw(ArgumentError("column indices J[k] must satisfy 1 <= J[k] <= n"))
end
csrk = csrrowptr[Ik+1]
csrrowptr[Ik+1] = csrk+1
csrcolval[csrk] = Jk
csrnzval[csrk] = V[k]
end
# This completes the unsorted-row, has-repeats CSR form's construction

# Sweep through the CSR form, simultaneously (1) caculating the CSC form's column
# counts and storing them shifted forward by one in csccolptr; (2) detecting repeated
# entries; and (3) repacking the CSR form with the repeated entries combined.
#
# Minimizing extraneous communication and nonlocality of reference, primarily by using
# only a single auxiliary array in this step, is the key to this method's performance.
fill!(csccolptr, 0)
fill!(klasttouch, 0)
writek = 1
newcsrrowptri = 1
origcsrrowptri = 1
origcsrrowptrip1 = csrrowptr[2]
@inbounds for i in 1:m
for readk in origcsrrowptri:(origcsrrowptrip1-1)
j = csrcolval[readk]
if klasttouch[j] < newcsrrowptri
klasttouch[j] = writek
if writek != readk
csrcolval[writek] = j
csrnzval[writek] = csrnzval[readk]
end
writek += 1
csccolptr[j+1] += 1
else
klt = klasttouch[j]
csrnzval[klt] = combine(csrnzval[klt], csrnzval[readk])
end
end
newcsrrowptri = writek
origcsrrowptri = origcsrrowptrip1
origcsrrowptrip1 != writek && (csrrowptr[i+1] = writek)
i < m && (origcsrrowptrip1 = csrrowptr[i+2])
end

# Compute the CSC form's colptrs and store them shifted forward by one in csccolptr
countsum = 1
csccolptr[1] = 1
@inbounds for j in 2:(n+1)
overwritten = csccolptr[j]
csccolptr[j] = countsum
countsum += overwritten
end

# Now knowing the CSC form's entry count, resize cscrowval and cscnzval if necessary
cscnnz = countsum - 1
length(cscrowval) < cscnnz && resize!(cscrowval, cscnnz)
length(cscnzval) < cscnnz && resize!(cscnzval, cscnnz)

# Finally counting-sort the row and nonzero values from the CSR form into cscrowval and
# cscnzval. Tracking write positions in csccolptr corrects the column pointers.
@inbounds for i in 1:m
for csrk in csrrowptr[i]:(csrrowptr[i+1]-1)
j = csrcolval[csrk]
x = csrnzval[csrk]
csck = csccolptr[j+1]
csccolptr[j+1] = csck+1
cscrowval[csck] = i
cscnzval[csck] = x
end
end

SparseMatrixCSC(m, n, csccolptr, cscrowval, cscnzval)
end
function sparse!{Tv,Ti<:Integer}(I::AbstractVector{Ti}, J::AbstractVector{Ti},
V::AbstractVector{Tv}, m::Integer, n::Integer, combine, klasttouch::Vector{Ti},
csrrowptr::Vector{Ti}, csrcolval::Vector{Ti}, csrnzval::Vector{Tv},
csccolptr::Vector{Ti} )
sparse!(I, J, V, m, n, combine, klasttouch,
csrrowptr, csrcolval, csrnzval,
csccolptr, Vector{Ti}(), Vector{Tv}() )
end
function sparse!{Tv,Ti<:Integer}(I::AbstractVector{Ti}, J::AbstractVector{Ti},
V::AbstractVector{Tv}, m::Integer, n::Integer, combine, klasttouch::Vector{Ti},
csrrowptr::Vector{Ti}, csrcolval::Vector{Ti}, csrnzval::Vector{Tv} )
sparse!(I, J, V, m, n, combine, klasttouch,
csrrowptr, csrcolval, csrnzval,
Vector{Ti}(n+1), Vector{Ti}(), Vector{Tv}() )
end

dimlub(I) = isempty(I) ? 0 : Int(maximum(I)) #least upper bound on required sparse matrix dimension

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13 changes: 11 additions & 2 deletions test/sparsedir/sparse.jl
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Expand Up @@ -8,6 +8,13 @@ using Base.Test

# check sparse matrix construction
@test isequal(full(sparse(complex(ones(5,5),ones(5,5)))), complex(ones(5,5),ones(5,5)))
@test_throws ArgumentError sparse([1,2,3], [1,2], [1,2,3], 3, 3)
@test_throws ArgumentError sparse([1,2,3], [1,2,3], [1,2], 3, 3)
@test_throws ArgumentError sparse([1,2,3], [1,2,3], [1,2,3], 0, 1)
@test_throws ArgumentError sparse([1,2,3], [1,2,3], [1,2,3], 1, 0)
@test_throws ArgumentError sparse([1,2,4], [1,2,3], [1,2,3], 3, 3)
@test_throws ArgumentError sparse([1,2,3], [1,2,4], [1,2,3], 3, 3)
@test isequal(sparse(Int[], Int[], Int[], 0, 0), SparseMatrixCSC(0, 0, Int[1], Int[], Int[]))

# check matrix operations
se33 = speye(3)
Expand Down Expand Up @@ -303,7 +310,8 @@ mfe22 = eye(Float64, 2)
@test_throws ArgumentError sparsevec([3,5,7],[0.1,0.0,3.2],4)

# issue #5169
@test nnz(sparse([1,1],[1,2],[0.0,-0.0])) == 0
# @test nnz(sparse([1,1],[1,2],[0.0,-0.0])) == 0
# commented following change to sparse() in #14798, also see #12605, #9928, #9906, #6769

# issue #5386
K,J,V = findnz(SparseMatrixCSC(2,1,[1,3],[1,2],[1.0,0.0]))
Expand All @@ -314,7 +322,8 @@ A = speye(Bool, 5)
@test find(A) == find(x -> x == true, A) == find(full(A))

# issue #5437
@test nnz(sparse([1,2,3],[1,2,3],[0.0,1.0,2.0])) == 2
# @test nnz(sparse([1,2,3],[1,2,3],[0.0,1.0,2.0])) == 2
# commented following change to sparse() in #14798, also see #12605, #9928, #9906, #6769

# issue #5824
@test sprand(4,5,0.5).^0 == sparse(ones(4,5))
Expand Down

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