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RFC: Reintroduce nnz and nonzeros #6963

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May 27, 2014
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RFC: Reintroduce nnz and nonzeros #6963

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4 changes: 2 additions & 2 deletions NEWS.md
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Expand Up @@ -320,7 +320,7 @@ Deprecated or removed

* `factorize!` is deprecated in favor of `factorize`. ([#5526])

* `nnz` is removed. Use `countnz` or `nfilled` instead ([#5538])
* `nnz` counts the number of structural nonzeros in a sparse matrix. Use `countnz` for the actual number of nonzeros. ([#6769])
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There's also a link farther down for the issue [#5538]

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Updated the link as well.

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I think it is more accurate to replace counts with returns:

nnz returns the number of structural nonzeros ...

This method is not doing the counting.


* `setfield` is renamed `setfield!` ([#5748])

Expand Down Expand Up @@ -383,7 +383,7 @@ Deprecated or removed
[#4888]: https://github.com/JuliaLang/julia/pull/4888
[#5475]: https://github.com/JuliaLang/julia/pull/5475
[#5526]: https://github.com/JuliaLang/julia/pull/5526
[#5538]: https://github.com/JuliaLang/julia/pull/5538
[#6769]: https://github.com/JuliaLang/julia/pull/6769
[#5726]: https://github.com/JuliaLang/julia/pull/5726
[#5811]: https://github.com/JuliaLang/julia/pull/5811
[#5462]: https://github.com/JuliaLang/julia/pull/5462
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1 change: 0 additions & 1 deletion base/abstractarray.jl
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Expand Up @@ -19,7 +19,6 @@ isreal{T<:Real,n}(x::AbstractArray{T,n}) = true
ndims{T,n}(::AbstractArray{T,n}) = n
ndims{T,n}(::Type{AbstractArray{T,n}}) = n
ndims{T<:AbstractArray}(::Type{T}) = ndims(super(T))
nfilled(t::AbstractArray) = length(t)
length(t::AbstractArray) = prod(size(t))::Int
endof(a::AbstractArray) = length(a)
first(a::AbstractArray) = a[1]
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18 changes: 0 additions & 18 deletions base/array.jl
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Expand Up @@ -1102,24 +1102,6 @@ function findnz{T}(A::StridedMatrix{T})
return (I, J, NZs)
end

function nonzeros{T}(A::StridedArray{T})
nnzA = countnz(A)
V = similar(A, T, nnzA)
count = 1
if nnzA > 0
for i=1:length(A)
Ai = A[i]
if Ai != 0
V[count] = Ai
count += 1
end
end
end
return V
end

nonzeros(x::Number) = x == 0 ? Array(typeof(x),0) : [x]

function findmax(a)
if isempty(a)
error("array must be non-empty")
Expand Down
2 changes: 0 additions & 2 deletions base/bitarray.jl
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Expand Up @@ -1385,8 +1385,6 @@ function findnz(B::BitMatrix)
return I, J, trues(length(I))
end

nonzeros(B::BitArray) = trues(countnz(B))

## Reductions ##

sum(A::BitArray, region) = reducedim(+, A, region, 0, Array(Int,reduced_dims(A,region)))
Expand Down
17 changes: 11 additions & 6 deletions base/deprecated.jl
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Expand Up @@ -380,6 +380,17 @@ end
export mmread

# 0.3 deprecations

function nfilled(X)
depwarn("nfilled has been renamed to nnz", :nfilled)
nnz(X)
end
export nfilled

@deprecate nonzeros(A::StridedArray) A[find(A)]
@deprecate nonzeros(B::BitArray) trues(countnz(B))
@deprecate nnz(A::StridedArray) countnz(A)

@deprecate dense full

export Stat
Expand Down Expand Up @@ -448,12 +459,6 @@ Set{T<:Number}(xs::T...) = Set{T}(xs)

# 0.3 discontinued functions

function nnz(X)
depwarn("nnz has been renamed to countnz and is no longer computed in constant time for sparse matrices. Instead, use nfilled() for the number of elements in a sparse matrix.", :nnz)
countnz(X)
end
export nnz

scale!{T<:Base.LinAlg.BlasReal}(X::Array{T}, s::Complex) = error("scale!: Cannot scale a real array by a complex value in-place. Use scale(X::Array{Real}, s::Complex) instead.")

@deprecate which(f::Callable, args...) @which f(args...)
2 changes: 1 addition & 1 deletion base/exports.jl
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Expand Up @@ -536,7 +536,7 @@ export
minimum,
minmax,
ndims,
nfilled,
nnz,
nonzeros,
nthperm!,
nthperm,
Expand Down
4 changes: 2 additions & 2 deletions base/linalg/cholmod.jl
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Expand Up @@ -14,7 +14,7 @@ export # types
using Base.LinAlg.UMFPACK # for decrement, increment, etc.

import Base: (*), convert, copy, ctranspose, eltype, findnz, getindex, hcat,
isvalid, nfilled, show, size, sort!, transpose, vcat
isvalid, nnz, show, size, sort!, transpose, vcat

import ..LinAlg: (\), A_mul_Bc, A_mul_Bt, Ac_ldiv_B, Ac_mul_B, At_ldiv_B, At_mul_B,
cholfact, cholfact!, copy, det, diag,
Expand Down Expand Up @@ -778,7 +778,7 @@ for Ti in (:Int32,:Int64)
(Ptr{c_CholmodSparse{Tv,$Ti}},Ptr{c_CholmodSparse{Tv,$Ti}},Cint,Ptr{Uint8}),
&A.c,&B.c,true,cmn($Ti))
end
function nfilled{Tv<:CHMVTypes}(A::CholmodSparse{Tv,$Ti})
function nnz{Tv<:CHMVTypes}(A::CholmodSparse{Tv,$Ti})
ccall((@chm_nm "nnz" $Ti
,:libcholmod), Int, (Ptr{c_CholmodSparse{Tv,$Ti}},Ptr{Uint8}),&A.c,cmn($Ti))
end
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12 changes: 6 additions & 6 deletions base/linalg/sparse.jl
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Expand Up @@ -347,7 +347,7 @@ function sparse_diff1{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti})
m,n = size(S)
m > 1 || return SparseMatrixCSC{Tv,Ti}(0, n, ones(n+1), Ti[], Tv[])
colptr = Array(Ti, n+1)
numnz = 2 * nfilled(S) # upper bound; will shrink later
numnz = 2 * nnz(S) # upper bound; will shrink later
rowval = Array(Ti, numnz)
nzval = Array(Tv, numnz)
numnz = 0
Expand Down Expand Up @@ -387,7 +387,7 @@ function sparse_diff2{Tv,Ti}(a::SparseMatrixCSC{Tv,Ti})

m,n = size(a)
colptr = Array(Ti, max(n,1))
numnz = 2 * nfilled(a) # upper bound; will shrink later
numnz = 2 * nnz(a) # upper bound; will shrink later
rowval = Array(Ti, numnz)
nzval = Array(Tv, numnz)

Expand Down Expand Up @@ -516,8 +516,8 @@ end
# kron

function kron{Tv,Ti}(a::SparseMatrixCSC{Tv,Ti}, b::SparseMatrixCSC{Tv,Ti})
numnzA = nfilled(a)
numnzB = nfilled(b)
numnzA = nnz(a)
numnzB = nnz(b)

numnz = numnzA * numnzB

Expand Down Expand Up @@ -593,7 +593,7 @@ inv(A::SparseMatrixCSC) = error("The inverse of a sparse matrix can often be den
function scale!{Tv,Ti}(C::SparseMatrixCSC{Tv,Ti}, A::SparseMatrixCSC, b::Vector)
m, n = size(A)
(n==length(b) && size(A)==size(C)) || throw(DimensionMismatch(""))
numnz = nfilled(A)
numnz = nnz(A)
C.colptr = convert(Array{Ti}, A.colptr)
C.rowval = convert(Array{Ti}, A.rowval)
C.nzval = Array(Tv, numnz)
Expand All @@ -606,7 +606,7 @@ end
function scale!{Tv,Ti}(C::SparseMatrixCSC{Tv,Ti}, b::Vector, A::SparseMatrixCSC)
m, n = size(A)
(n==length(b) && size(A)==size(C)) || throw(DimensionMismatch(""))
numnz = nfilled(A)
numnz = nnz(A)
C.colptr = convert(Array{Ti}, A.colptr)
C.rowval = convert(Array{Ti}, A.rowval)
C.nzval = Array(Tv, numnz)
Expand Down
2 changes: 1 addition & 1 deletion base/sparse.jl
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Expand Up @@ -7,7 +7,7 @@ import Base.NonTupleType, Base.float

export SparseMatrixCSC,
blkdiag, dense, diag, diagm, droptol!, dropzeros!, etree, full,
getindex, ishermitian, issparse, issym, istril, istriu,
getindex, ishermitian, issparse, issym, istril, istriu, nnz,
setindex!, sparse, sparsevec, spdiagm, speye, spones,
sprand, sprandbool, sprandn, spzeros, symperm, trace, tril, tril!,
triu, triu!
Expand Down
14 changes: 7 additions & 7 deletions base/sparse/csparse.jl
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Expand Up @@ -128,7 +128,7 @@ function transpose!{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti}, T::SparseMatrixCSC{Tv,Ti})
rowval_T = T.rowval
nzval_T = T.nzval

nnzS = nfilled(S)
nnzS = nnz(S)
colptr_S = S.colptr
rowval_S = S.rowval
nzval_S = S.nzval
Expand All @@ -147,15 +147,15 @@ end

function transpose{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti})
(nT, mT) = size(S)
nnzS = nfilled(S)
nnzS = nnz(S)
rowval_S = S.rowval

rowval_T = Array(Ti, nnzS)
nzval_T = Array(Tv, nnzS)

colptr_T = zeros(Ti, nT+1)
colptr_T[1] = 1
@inbounds for i=1:nfilled(S)
@inbounds for i=1:nnz(S)
colptr_T[rowval_S[i]+1] += 1
end
colptr_T = cumsum(colptr_T)
Expand All @@ -172,7 +172,7 @@ function ctranspose!{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti}, T::SparseMatrixCSC{Tv,Ti}
rowval_T = T.rowval
nzval_T = T.nzval

nnzS = nfilled(S)
nnzS = nnz(S)
colptr_S = S.colptr
rowval_S = S.rowval
nzval_S = S.nzval
Expand All @@ -191,15 +191,15 @@ end

function ctranspose{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti})
(nT, mT) = size(S)
nnzS = nfilled(S)
nnzS = nnz(S)
rowval_S = S.rowval

rowval_T = Array(Ti, nnzS)
nzval_T = Array(Tv, nnzS)

colptr_T = zeros(Ti, nT+1)
colptr_T[1] = 1
@inbounds for i=1:nfilled(S)
@inbounds for i=1:nnz(S)
colptr_T[rowval_S[i]+1] += 1
end
colptr_T = cumsum(colptr_T)
Expand Down Expand Up @@ -335,7 +335,7 @@ end
# Section 2.7: Removing entries from a matrix
# http://www.cise.ufl.edu/research/sparse/CSparse/
function fkeep!{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, f, other)
nzorig = nfilled(A)
nzorig = nnz(A)
nz = 1
for j = 1:A.n
p = A.colptr[j] # record current position
Expand Down
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