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linalg_dense.jl
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linalg_dense.jl
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# Linear algebra functions for dense matrices in column major format
scale!(X::Array{Float32}, s::Real) = BLAS.scal!(numel(X), float32(s), X, 1)
scale!(X::Array{Float64}, s::Real) = BLAS.scal!(numel(X), float64(s), X, 1)
scale!(X::Array{Complex64}, s::Real) = (ccall(("sscal_",Base.libblas_name), Void, (Ptr{BlasInt}, Ptr{Float32}, Ptr{Complex64}, Ptr{BlasInt}), &(2*numel(X)), &s, X, &1); X)
scale!(X::Array{Complex128}, s::Real) = (ccall(("dscal_",Base.libblas_name), Void, (Ptr{BlasInt}, Ptr{Float64}, Ptr{Complex128}, Ptr{BlasInt}), &(2*numel(X)), &s, X, &1); X)
#Test whether a matrix is positive-definite
isposdef!{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = LAPACK.potrf!(UL, A)[2] == 0
isposdef!(A::Matrix) = ishermitian(A) && isposdef!(A, 'U')
isposdef{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = isposdef!(copy(A), UL)
isposdef{T<:BlasFloat}(A::Matrix{T}) = isposdef!(copy(A))
isposdef{T<:Number}(A::Matrix{T}, UL::BlasChar) = isposdef!(float64(A), UL)
isposdef{T<:Number}(A::Matrix{T}) = isposdef!(float64(A))
isposdef(x::Number) = imag(x)==0 && real(x) > 0
norm{T<:BlasFloat}(x::Vector{T}) = BLAS.nrm2(length(x), x, 1)
function norm{T<:BlasFloat, TI<:Integer}(x::Vector{T}, rx::Union(Range1{TI},Range{TI}))
if min(rx) < 1 || max(rx) > length(x)
throw(BoundsError())
end
BLAS.nrm2(length(rx), pointer(x)+(first(rx)-1)*sizeof(T), step(rx))
end
function triu!{T}(M::Matrix{T}, k::Integer)
m, n = size(M)
idx = 1
for j = 0:n-1
ii = min(max(0, j+1-k), m)
for i = (idx+ii):(idx+m-1)
M[i] = zero(T)
end
idx += m
end
return M
end
triu(M::Matrix, k::Integer) = triu!(copy(M), k)
function tril!{T}(M::Matrix{T}, k::Integer)
m, n = size(M)
idx = 1
for j = 0:n-1
ii = min(max(0, j-k), m)
for i = idx:(idx+ii-1)
M[i] = zero(T)
end
idx += m
end
return M
end
tril(M::Matrix, k::Integer) = tril!(copy(M), k)
diff(a::Vector) = [ a[i+1] - a[i] for i=1:length(a)-1 ]
function diff(a::Matrix, dim::Integer)
if dim == 1
[ a[i+1,j] - a[i,j] for i=1:size(a,1)-1, j=1:size(a,2) ]
else
[ a[i,j+1] - a[i,j] for i=1:size(a,1), j=1:size(a,2)-1 ]
end
end
function gradient(F::Vector, h::Vector)
n = length(F)
g = similar(F)
if n > 0
g[1] = 0
end
if n > 1
g[1] = (F[2] - F[1]) / (h[2] - h[1])
g[n] = (F[n] - F[n-1]) / (h[end] - h[end-1])
end
if n > 2
h = h[3:n] - h[1:n-2]
g[2:n-1] = (F[3:n] - F[1:n-2]) ./ h
end
return g
end
function diag{T}(A::Matrix{T}, k::Integer)
m, n = size(A)
if k >= 0 && k < n
nV = min(m, n-k)
elseif k < 0 && -k < m
nV = min(m+k, n)
else
throw(BoundsError())
end
V = zeros(T, nV)
if k > 0
for i=1:nV
V[i] = A[i, i+k]
end
else
for i=1:nV
V[i] = A[i-k, i]
end
end
return V
end
diag(A) = diag(A, 0)
function diagm{T}(v::VecOrMat{T}, k::Integer)
if isa(v, Matrix)
if (size(v,1) != 1 && size(v,2) != 1)
error("Input should be nx1 or 1xn")
end
end
n = numel(v)
if k >= 0
a = zeros(T, n+k, n+k)
for i=1:n
a[i,i+k] = v[i]
end
else
a = zeros(T, n-k, n-k)
for i=1:n
a[i-k,i] = v[i]
end
end
return a
end
diagm(v) = diagm(v, 0)
diagm(x::Number) = (X = Array(typeof(x),1,1); X[1,1] = x; X)
function trace{T}(A::Matrix{T})
t = zero(T)
for i=1:min(size(A))
t += A[i,i]
end
return t
end
kron(a::Vector, b::Vector) = [ a[i]*b[j] for i=1:length(a), j=1:length(b) ]
function kron{T,S}(a::Matrix{T}, b::Matrix{S})
R = Array(promote_type(T,S), size(a,1)*size(b,1), size(a,2)*size(b,2))
m = 1
for j = 1:size(a,2)
for l = 1:size(b,2)
for i = 1:size(a,1)
aij = a[i,j]
for k = 1:size(b,1)
R[m] = aij*b[k,l]
m += 1
end
end
end
end
R
end
kron(a::Number, b::Number) = a * b
kron(a::Vector, b::Number) = a * b
kron(a::Number, b::Vector) = a * b
kron(a::Matrix, b::Number) = a * b
kron(a::Number, b::Matrix) = a * b
function randsym(n)
a = randn(n,n)
for j=1:n-1, i=j+1:n
x = (a[i,j]+a[j,i])/2
a[i,j] = x
a[j,i] = x
end
a
end
^(A::Matrix, p::Integer) = p < 0 ? inv(A^-p) : power_by_squaring(A,p)
function ^(A::Matrix, p::Number)
if integer_valued(p)
ip = integer(real(p))
if ip < 0
return inv(power_by_squaring(A, -ip))
else
return power_by_squaring(A, ip)
end
end
if size(A,1) != size(A,2)
error("matrix must be square")
end
(v, X) = eig(A)
if isreal(v) && any(v.<0)
v = complex(v)
end
if ishermitian(A)
Xinv = X'
else
Xinv = inv(X)
end
diagmm(X, v.^p)*Xinv
end
function rref{T}(A::Matrix{T})
nr, nc = size(A)
U = copy_to(similar(A, T <: Complex ? Complex128 : Float64), A)
e = eps(norm(U,Inf))
i = j = 1
while i <= nr && j <= nc
(m, mi) = findmax(abs(U[i:nr,j]))
mi = mi+i - 1
if m <= e
U[i:nr,j] = 0
j += 1
else
for k=j:nc
U[i, k], U[mi, k] = U[mi, k], U[i, k]
end
d = U[i,j]
for k = j:nc
U[i,k] /= d
end
for k = 1:nr
if k != i
d = U[k,j]
for l = j:nc
U[k,l] -= d*U[i,l]
end
end
end
i += 1
j += 1
end
end
return U
end
rref(x::Number) = one(x)
## Destructive matrix exponential using algorithm from Higham, 2008,
## "Functions of Matrices: Theory and Computation", SIAM
function expm!{T<:BlasFloat}(A::StridedMatrix{T})
m, n = size(A)
if m != n error("expm!: Matrix A must be square") end
if m < 2 return exp(A) end
ilo, ihi, scale = LAPACK.gebal!('B', A) # modifies A
nA = norm(A, 1)
I = eye(T,n)
## For sufficiently small nA, use lower order Padé-Approximations
if (nA <= 2.1)
if nA > 0.95
C = T[17643225600.,8821612800.,2075673600.,302702400.,
30270240., 2162160., 110880., 3960.,
90., 1.]
elseif nA > 0.25
C = T[17297280.,8648640.,1995840.,277200.,
25200., 1512., 56., 1.]
elseif nA > 0.015
C = T[30240.,15120.,3360.,
420., 30., 1.]
else
C = T[120.,60.,12.,1.]
end
A2 = A * A
P = copy(I)
# U = C[2] * P
# V = C[1] * P
U = zeros(T, n, n)
V = zeros(T, n, n)
C2 = C[2]; C1 = C[1]
for i=1:n
U[i,i] = C2
V[i,i] = C1
end
for k in 1:(div(size(C, 1), 2) - 1)
k2 = 2 * k
P *= A2
#U += C[k2 + 2] * P
#V += C[k2 + 1] * P
Ck21 = C[k2 + 1]
Ck22 = C[k2 + 2]
for i=1:length(P)
U[i] += Ck22 * P[i]
V[i] += Ck21 * P[i]
end
end
U = A * U
#X = (V - U)\(V + U)
X = V + U
LAPACK.gesv!(V-U, X)
else
s = log2(nA/5.4) # power of 2 later reversed by squaring
if s > 0
si = iceil(s)
A /= oftype(T,2^si)
end
CC = T[64764752532480000.,32382376266240000.,7771770303897600.,
1187353796428800., 129060195264000., 10559470521600.,
670442572800., 33522128640., 1323241920.,
40840800., 960960., 16380.,
182., 1.]
A2 = A * A
A4 = A2 * A2
A6 = A2 * A4
# U = A * (A6 * (CC[14]*A6 + CC[12]*A4 + CC[10]*A2) +
# CC[8]*A6 + CC[6]*A4 + CC[4]*A2 + CC[2]*I)
# V = A6 * (CC[13]*A6 + CC[11]*A4 + CC[9]*A2) +
# CC[7]*A6 + CC[5]*A4 + CC[3]*A2 + CC[1]*I
P1 = zeros(T, n, n)
P2 = zeros(T, n, n)
P3 = zeros(T, n, n)
P4 = zeros(T, n, n)
CC14 = CC[14]; CC12 = CC[12]; CC10 = CC[10]
CC8 = CC[8]; CC6 = CC[6]; CC4 = CC[4]; CC2 = CC[2]
CC13 = CC[13]; CC11 = CC[11]; CC9 = CC[9]
CC7 = CC[7]; CC5 = CC[5]; CC3 = CC[3]; CC1 = CC[1]
for i=1:length(I)
P1[i] += CC14*A6[i] + CC12*A4[i] + CC10*A2[i]
P2[i] += CC8*A6[i] + CC6*A4[i] + CC4*A2[i] + CC2*I[i]
P3[i] += CC13*A6[i] + CC11*A4[i] + CC9*A2[i]
P4[i] += CC7*A6[i] + CC5*A4[i] + CC3*A2[i] + CC1*I[i]
end
#U = A * (A6*P1 + P2)
#V = A6*P3 + P4
U = A * (BLAS.gemm!('N', 'N', one(T), A6, P1, one(T), P2))
V = BLAS.gemm!('N', 'N', one(T), A6, P3, one(T), P4)
#X = (V-U)\(V+U)
X = V + U
LAPACK.gesv!(V-U, X)
if s > 0 # squaring to reverse dividing by power of 2
for t in 1:si X *= X end
end
end
# Undo the balancing
doscale = false # check if rescaling is needed
for i = ilo:ihi
if scale[i] != 1.
doscale = true
break
end
end
if doscale
for j = ilo:ihi
scj = scale[j]
if scj != 1. # is this overkill?
for i = ilo:ihi
X[i,j] *= scale[i]/scj
end
else
for i = ilo:ihi
X[i,j] *= scale[i]
end
end
end
end
if ilo > 1 # apply lower permutations in reverse order
for j in (ilo-1):1:-1 rcswap!(j, int(scale[j]), X) end
end
if ihi < n # apply upper permutations in forward order
for j in (ihi+1):n rcswap!(j, int(scale[j]), X) end
end
X
end
## Swap rows j and jp and columns j and jp in X
function rcswap!{T<:Number}(j::Integer, jp::Integer, X::StridedMatrix{T})
for k in 1:size(X, 2)
tmp = X[k,j]
X[k,j] = X[k,jp]
X[k,jp] = tmp
tmp = X[j,k]
X[j,k] = X[jp,k]
X[jp,k] = tmp
end
end
# Matrix exponential
expm{T<:Union(Float32,Float64,Complex64,Complex128)}(A::StridedMatrix{T}) = expm!(copy(A))
expm{T<:Integer}(A::StridedMatrix{T}) = expm!(float(A))
expm(x::Number) = exp(x)
## Matrix factorizations and decompositions
abstract Factorization{T}
## Create an extractor that extracts the modified original matrix, e.g.
## LD for BunchKaufman, LR for CholeskyDense, LU for LUDense and
## define size methods for Factorization types using it.
type BunchKaufman{T<:BlasFloat} <: Factorization{T}
LD::Matrix{T}
ipiv::Vector{BlasInt}
UL::BlasChar
function BunchKaufman(A::Matrix{T}, UL::BlasChar)
LD, ipiv = LAPACK.sytrf!(UL , copy(A))
new(LD, ipiv, UL)
end
end
BunchKaufman{T<:BlasFloat}(A::StridedMatrix{T}, UL::BlasChar) = BunchKaufman{T}(A, UL)
BunchKaufman{T<:Real}(A::StridedMatrix{T}, UL::BlasChar) = BunchKaufman(float64(A), UL)
BunchKaufman{T<:Number}(A::StridedMatrix{T}) = BunchKaufman(A, 'U')
size(B::BunchKaufman) = size(B.LD)
size(B::BunchKaufman,d::Integer) = size(B.LD,d)
## need to work out how to extract the factors.
#factors(B::BunchKaufman) = LAPACK.syconv!(B.UL, copy(B.LD), B.ipiv)
function inv(B::BunchKaufman)
symmetrize!(LAPACK.sytri!(B.UL, copy(B.LD), B.ipiv), B.UL)
end
\{T<:BlasFloat}(B::BunchKaufman{T}, R::StridedVecOrMat{T}) =
LAPACK.sytrs!(B.UL, B.LD, B.ipiv, copy(R))
type CholeskyDense{T<:BlasFloat} <: Factorization{T}
LR::Matrix{T}
UL::BlasChar
function CholeskyDense(A::Matrix{T}, UL::BlasChar)
A, info = LAPACK.potrf!(UL, A)
if info != 0 error("Matrix A not positive-definite") end
if UL == 'U'
new(triu!(A), UL)
elseif UL == 'L'
new(tril!(A), UL)
else
error("Second argument UL should be 'U' or 'L'")
end
end
end
size(C::CholeskyDense) = size(C.LR)
size(C::CholeskyDense,d::Integer) = size(C.LR,d)
factors(C::CholeskyDense) = C.LR
\{T<:BlasFloat}(C::CholeskyDense{T}, B::StridedVecOrMat{T}) =
LAPACK.potrs!(C.UL, C.LR, copy(B))
function det{T}(C::CholeskyDense{T})
ff = C.LR
dd = one(T)
for i in 1:size(ff,1) dd *= abs2(ff[i,i]) end
dd
end
function inv(C::CholeskyDense)
Ci, info = LAPACK.potri!(C.UL, copy(C.LR))
if info != 0 error("Matrix singular") end
symmetrize!(Ci, C.UL)
end
## Should these functions check that the matrix is Hermitian?
chold!{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = CholeskyDense{T}(A, UL)
chold!{T<:BlasFloat}(A::Matrix{T}) = chold!(A, 'U')
chold{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = chold!(copy(A), UL)
chold{T<:Number}(A::Matrix{T}, UL::BlasChar) = chold(float64(A), UL)
chold{T<:Number}(A::Matrix{T}) = chold(A, 'U')
## Matlab (and R) compatible
chol(A::Matrix, UL::BlasChar) = factors(chold(A, UL))
chol(A::Matrix) = chol(A, 'U')
chol(x::Number) = imag(x) == 0 && real(x) > 0 ? sqrt(x) : error("Argument not positive-definite")
type CholeskyDensePivoted{T<:BlasFloat} <: Factorization{T}
LR::Matrix{T}
UL::BlasChar
piv::Vector{BlasInt}
rank::BlasInt
tol::Real
function CholeskyDensePivoted(A::Matrix{T}, UL::BlasChar, tol::Real)
A, piv, rank, info = LAPACK.pstrf!(UL, A, tol)
if UL == 'U'
new(triu!(A), UL, piv, rank, tol)
elseif UL == 'L'
new(tril!(A), UL, piv, rank, tol)
else
error("Second argument UL should be 'U' or 'L'")
end
end
end
size(C::CholeskyDensePivoted) = size(C.LR)
size(C::CholeskyDensePivoted,d::Integer) = size(C.LR,d)
factors(C::CholeskyDensePivoted) = C.LR, C.piv
function \{T<:BlasFloat}(C::CholeskyDensePivoted{T}, B::StridedVector{T})
if C.rank < size(C.LR, 1) error("Matrix is not positive-definite") end
LAPACK.potrs!(C.UL, C.LR, copy(B)[C.piv])[invperm(C.piv)]
end
function \{T<:BlasFloat}(C::CholeskyDensePivoted{T}, B::StridedMatrix{T})
if C.rank < size(C.LR, 1) error("Matrix is not positive-definite") end
LAPACK.potrs!(C.UL, C.LR, copy(B)[C.piv,:])[invperm(C.piv),:]
end
rank(C::CholeskyDensePivoted) = C.rank
function det{T}(C::CholeskyDensePivoted{T})
if C.rank < size(C.LR, 1)
return real(zero(T))
else
return prod(abs2(diag(C.LR)))
end
end
function inv(C::CholeskyDensePivoted)
if C.rank < size(C.LR, 1) error("Matrix singular") end
Ci, info = LAPACK.potri!(C.UL, copy(C.LR))
if info != 0 error("Matrix is singular") end
ipiv = invperm(C.piv)
(symmetrize!(Ci, C.UL))[ipiv, ipiv]
end
## Should these functions check that the matrix is Hermitian?
cholpd!{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar, tol::Real) = CholeskyDensePivoted{T}(A, UL, tol)
cholpd!{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = cholpd!(A, UL, -1.)
cholpd!{T<:BlasFloat}(A::Matrix{T}, tol::Real) = cholpd!(A, 'U', tol)
cholpd!{T<:BlasFloat}(A::Matrix{T}) = cholpd!(A, 'U', -1.)
cholpd{T<:Number}(A::Matrix{T}, UL::BlasChar, tol::Real) = cholpd(float64(A), UL, tol)
cholpd{T<:Number}(A::Matrix{T}, UL::BlasChar) = cholpd(float64(A), UL, -1.)
cholpd{T<:Number}(A::Matrix{T}, tol::Real) = cholpd(float64(A), true, tol)
cholpd{T<:Number}(A::Matrix{T}) = cholpd(float64(A), 'U', -1.)
cholpd{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar, tol::Real) = cholpd!(copy(A), UL, tol)
cholpd{T<:BlasFloat}(A::Matrix{T}, UL::BlasChar) = cholpd!(copy(A), UL, -1.)
cholpd{T<:BlasFloat}(A::Matrix{T}, tol::Real) = cholpd!(copy(A), 'U', tol)
cholpd{T<:BlasFloat}(A::Matrix{T}) = cholpd!(copy(A), 'U', -1.)
type LUDense{T} <: Factorization{T}
lu::Matrix{T}
ipiv::Vector{BlasInt}
info::BlasInt
function LUDense(lu::Matrix{T}, ipiv::Vector{BlasInt}, info::BlasInt)
m, n = size(lu)
m == n ? new(lu, ipiv, info) : error("LUDense only defined for square matrices")
end
end
size(A::LUDense) = size(A.lu)
size(A::LUDense,n) = size(A.lu,n)
function factors{T}(lu::LUDense{T})
LU, ipiv = lu.lu, lu.ipiv
m, n = size(LU)
L = m >= n ? tril(LU, -1) + eye(T,m,n) : tril(LU, -1)[:, 1:m] + eye(T,m)
U = m <= n ? triu(LU) : triu(LU)[1:n, :]
P = [1:m]
for i = 1:min(m,n)
t = P[i]
P[i] = P[ipiv[i]]
P[ipiv[i]] = t
end
L, U, P
end
function lud!{T<:BlasFloat}(A::Matrix{T})
lu, ipiv, info = LAPACK.getrf!(A)
LUDense{T}(lu, ipiv, info)
end
lud{T<:BlasFloat}(A::Matrix{T}) = lud!(copy(A))
lud{T<:Number}(A::Matrix{T}) = lud(float64(A))
## Matlab-compatible
lu{T<:Number}(A::Matrix{T}) = factors(lud(A))
lu(x::Number) = (one(x), x, [1])
function det{T}(lu::LUDense{T})
m, n = size(lu)
if lu.info > 0; return zero(typeof(lu.lu[1])); end
prod(diag(lu.lu)) * (bool(sum(lu.ipiv .!= 1:n) % 2) ? -one(T) : one(T))
end
function det(A::Matrix)
m, n = size(A)
if m != n; error("det only defined for square matrices"); end
if istriu(A) | istril(A); return prod(diag(A)); end
return det(lud(A))
end
det(x::Number) = x
function (\){T<:BlasFloat}(lu::LUDense{T}, B::StridedVecOrMat{T})
if lu.info > 0; throw(LAPACK.SingularException(info)); end
LAPACK.getrs!('N', lu.lu, lu.ipiv, copy(B))
end
function inv{T<:BlasFloat}(lu::LUDense{T})
m, n = size(lu.lu)
if m != n; error("inv only defined for square matrices"); end
if lu.info > 0; return throw(LAPACK.SingularException(info)); end
LAPACK.getri!(copy(lu.lu), lu.ipiv)
end
## QR decomposition without column pivots
type QRDense{T} <: Factorization{T}
hh::Matrix{T} # Householder transformations and R
tau::Vector{T} # Scalar factors of transformations
function QRDense(hh::Matrix{T}, tau::Vector{T})
numel(tau) == min(size(hh)) ? new(hh, tau) : error("QR: mismatched dimensions")
end
end
size(A::QRDense) = size(A.hh)
size(A::QRDense,n) = size(A.hh,n)
qrd!{T<:BlasFloat}(A::StridedMatrix{T}) = QRDense{T}(LAPACK.geqrf!(A)...)
qrd{T<:BlasFloat}(A::StridedMatrix{T}) = qrd!(copy(A))
qrd{T<:Real}(A::StridedMatrix{T}) = qrd(float64(A))
function factors{T<:BlasFloat}(qrd::QRDense{T})
aa = copy(qrd.hh)
R = triu(aa[1:min(size(aa)),:]) # must be *before* call to orgqr!
LAPACK.orgqr!(aa, qrd.tau, size(aa,2)), R
end
qr{T<:Number}(x::StridedMatrix{T}) = factors(qrd(x))
qr(x::Number) = (one(x), x)
## Multiplication by Q from the QR decomposition
(*){T<:BlasFloat}(A::QRDense{T}, B::StridedVecOrMat{T}) =
LAPACK.ormqr!('L', 'N', A.hh, size(A.hh,2), A.tau, copy(B))
## Multiplication by Q' from the QR decomposition
Ac_mul_B{T<:BlasFloat}(A::QRDense{T}, B::StridedVecOrMat{T}) =
LAPACK.ormqr!('L', iscomplex(A.tau)?'C':'T', A.hh, size(A.hh,2), A.tau, copy(B))
## Least squares solution. Should be more careful about cases with m < n
function (\){T<:BlasFloat}(A::QRDense{T}, B::StridedVecOrMat{T})
n = length(A.tau)
ans, info = LAPACK.trtrs!('U','N','N',A.hh[1:n,:],(A'*B)[1:n,:])
if info > 0; throw(LAPACK.SingularException(info)); end
return ans
end
type QRPDense{T} <: Factorization{T}
hh::Matrix{T}
tau::Vector{T}
jpvt::Vector{BlasInt}
function QRPDense(hh::Matrix{T}, tau::Vector{T}, jpvt::Vector{BlasInt})
m, n = size(hh)
if length(tau) != min(m,n) || length(jpvt) != n
error("QRPDense: mismatched dimensions")
end
new(hh,tau,jpvt)
end
end
size(x::QRPDense) = size(x.hh)
size(x::QRPDense,d) = size(x.hh,d)
## Multiplication by Q from the QR decomposition
(*){T<:BlasFloat}(A::QRPDense{T}, B::StridedVecOrMat{T}) =
LAPACK.ormqr!('L', 'N', A.hh, size(A,2), A.tau, copy(B))
## Multiplication by Q' from the QR decomposition
Ac_mul_B{T<:BlasFloat}(A::QRPDense{T}, B::StridedVecOrMat{T}) =
LAPACK.ormqr!('L', iscomplex(A.tau)?'C':'T', A.hh, size(A,2), A.tau, copy(B))
qrpd!{T<:BlasFloat}(A::StridedMatrix{T}) = QRPDense{T}(LAPACK.geqp3!(A)...)
qrpd{T<:BlasFloat}(A::StridedMatrix{T}) = qrpd!(copy(A))
qrpd{T<:Real}(x::StridedMatrix{T}) = qrpd(float64(x))
function factors{T<:BlasFloat}(x::QRPDense{T})
aa = copy(x.hh)
R = triu(aa[1:min(size(aa)),:])
LAPACK.orgqr!(aa, x.tau, size(aa,2)), R, x.jpvt
end
qrp{T<:BlasFloat}(x::StridedMatrix{T}) = factors(qrpd(x))
qrp{T<:Real}(x::StridedMatrix{T}) = qrp(float64(x))
function (\){T<:BlasFloat}(A::QRPDense{T}, B::StridedVecOrMat{T})
n = length(A.tau)
x, info = LAPACK.trtrs!('U','N','N',A.hh[1:n,:],(A'*B)[1:n,:])
if info > 0; throw(LAPACK.SingularException(info)); end
isa(B, Vector) ? x[invperm(A.jpvt)] : x[:,invperm(A.jpvt)]
end
function eig{T<:BlasFloat}(A::StridedMatrix{T}, vecs::Bool)
n = size(A, 2)
if n == 0; return vecs ? (zeros(T, 0), zeros(T, 0, 0)) : zeros(T, 0, 0); end
if ishermitian(A)
if vecs
Z = similar(A)
W = LAPACK.syevr!(copy(A), Z)
return W, Z
else
W = LAPACK.syevr!(copy(A))
return W
end
end
if iscomplex(A)
W, VR = LAPACK.geev!('N', vecs ? 'V' : 'N', copy(A))[2:3]
if vecs; return W, VR; end
return W
end
VL, WR, WI, VR = LAPACK.geev!('N', vecs ? 'V' : 'N', copy(A))
if all(WI .== 0.)
if vecs; return WR, VR; end
return WR
end
if vecs
evec = complex(zeros(T, n, n))
j = 1
while j <= n
if WI[j] == 0.0
evec[:,j] = VR[:,j]
else
evec[:,j] = VR[:,j] + im*VR[:,j+1]
evec[:,j+1] = VR[:,j] - im*VR[:,j+1]
j += 1
end
j += 1
end
return complex(WR, WI), evec
end
complex(WR, WI)
end
eig{T<:Integer}(x::StridedMatrix{T}, vecs::Bool) = eig(float64(x), vecs)
eig(x::Number, vecs::Bool) = vecs ? (x, one(x)) : x
eig(x) = eig(x, true)
eigvals(x) = eig(x, false)
# This is the svd based on the LAPACK GESVD, which is slower, but takes
# lesser memory. It should be made available through a keyword argument
# at a later date.
#
# function svd{T<:BlasFloat}(A::StridedMatrix{T},vecs::Bool,thin::Bool)
# m,n = size(A)
# if m == 0 || n == 0
# if vecs; return (eye(m, thin ? n : m), zeros(0), eye(n,n)); end
# return (zeros(T, 0, 0), zeros(T, 0), zeros(T, 0, 0))
# end
# if vecs; return LAPACK.gesvd!(thin ? 'S' : 'A', thin ? 'S' : 'A', copy(A)); end
# LAPACK.gesvd!('N', 'N', copy(A))
# end
#
# svd{T<:Integer}(x::StridedMatrix{T},vecs,thin) = svd(float64(x),vecs,thin)
# svd(A::StridedMatrix) = svd(A,true,false)
# svd(A::StridedMatrix, thin::Bool) = svd(A,true,thin)
# svdvals(A) = svd(A,false,true)[2]
function svd{T<:BlasFloat}(A::StridedMatrix{T},vecs::Bool,thin::Bool)
m,n = size(A)
if m == 0 || n == 0
if vecs; return (eye(m, thin ? n : m), zeros(0), eye(n,n)); end
return (zeros(T, 0, 0), zeros(T, 0), zeros(T, 0, 0))
end
if vecs; return LAPACK.gesdd!(thin ? 'S' : 'A', copy(A)); end
LAPACK.gesdd!('N', copy(A))
end
svd{T<:Integer}(x::StridedMatrix{T},vecs,thin) = svd(float64(x),vecs,thin)
svd(x::Number,vecs::Bool,thin::Bool) = vecs ? (x==0?one(x):x/abs(x),abs(x),one(x)) : ([],abs(x),[])
svd(A) = svd(A,true,false)
svd(A, thin::Bool) = svd(A,true,thin)
svdvals(A) = svd(A,false,true)[2]
function (\){T<:BlasFloat}(A::StridedMatrix{T}, B::StridedVecOrMat{T})
Acopy = copy(A)
m, n = size(Acopy)
X = copy(B)
if m == n # Square
if istriu(A)
ans, info = LAPACK.trtrs!('U', 'N', 'N', Acopy, X)
if info > 0; throw(LAPACK.SingularException(info)); end
return ans
end
if istril(A)
ans, info = LAPACK.trtrs!('L', 'N', 'N', Acopy, X)
if info > 0; throw(LAPACK.SingularException(info)); end
return ans
end
if ishermitian(A)
ans, _, _, info = LAPACK.sysv!('U', Acopy, X)
if info > 0; throw(LAPACK.SingularException(info)); end
return ans
end
ans, _, _, info = LAPACK.gesv!(Acopy, X)
if info > 0; throw(LAPACK.SingularException(info)); end
return ans
end
LAPACK.gelsd!(Acopy, X)[1]
end
(\){T1<:BlasFloat, T2<:BlasFloat}(A::StridedMatrix{T1}, B::StridedVecOrMat{T2}) =
(\)(convert(Array{promote_type(T1,T2)},A), convert(Array{promote_type(T1,T2)},B))
(\){T1<:BlasFloat, T2<:Real}(A::StridedMatrix{T1}, B::StridedVecOrMat{T2}) = (\)(A, convert(Array{T1}, B))
(\){T1<:Real, T2<:BlasFloat}(A::StridedMatrix{T1}, B::StridedVecOrMat{T2}) = (\)(convert(Array{T2}, A), B)
(\){T1<:Real, T2<:Real}(A::StridedMatrix{T1}, B::StridedVecOrMat{T2}) = (\)(float64(A), float64(B))
(\){T1<:Number, T2<:Number}(A::StridedMatrix{T1}, B::StridedVecOrMat{T2}) = (\)(complex128(A), complex128(B))
(/)(A::StridedVecOrMat, B::StridedVecOrMat) = (B' \ A')'
##TODO: Add methods for rank(A::QRP{T}) and adjust the (\) method accordingly
## Add rcond methods for Cholesky, LU, QR and QRP types
## Lower priority: Add LQ, QL and RQ factorizations
## Moore-Penrose inverse
function pinv{T<:BlasFloat}(A::StridedMatrix{T})
u,s,vt = svd(A, true)
sinv = zeros(T, length(s))
index = s .> eps(real(one(T)))*max(size(A))*max(s)
sinv[index] = 1 ./ s[index]
vt'diagmm(sinv, u')
end
pinv{T<:Integer}(A::StridedMatrix{T}) = pinv(float(A))
pinv(a::StridedVector) = pinv(reshape(a, length(a), 1))
pinv(x::Number) = one(x)/x
## Basis for null space
function null{T<:BlasFloat}(A::StridedMatrix{T})
m,n = size(A)
_,s,vt = svd(A)
if m == 0; return eye(T, n); end
indstart = sum(s .> max(m,n)*max(s)*eps(eltype(s))) + 1
vt[indstart:,:]'
end
null{T<:Integer}(A::StridedMatrix{T}) = null(float(A))
null(a::StridedVector) = null(reshape(a, length(a), 1))
function cond(A::StridedMatrix, p)
if p == 2
v = svdvals(A)
maxv = max(v)
cnd = maxv == 0.0 ? Inf : maxv / min(v)
elseif p == 1 || p == Inf
m, n = size(A)
if m != n; error("Use 2-norm for non-square matrices"); end
cnd = 1 / LAPACK.gecon!(p == 1 ? '1' : 'I', lud(A).lu, norm(A, p))
else
error("Norm type must be 1, 2 or Inf")
end
return cnd
end
cond(A::StridedMatrix) = cond(A, 2)
#### Specialized matrix types ####
## Symmetric tridiagonal matrices
type SymTridiagonal{T<:BlasFloat} <: AbstractMatrix{T}
dv::Vector{T} # diagonal
ev::Vector{T} # sub/super diagonal
function SymTridiagonal(dv::Vector{T}, ev::Vector{T})
if length(ev) != length(dv) - 1 error("dimension mismatch") end
new(dv,ev)
end
end
SymTridiagonal{T<:BlasFloat}(dv::Vector{T}, ev::Vector{T}) = SymTridiagonal{T}(copy(dv), copy(ev))
function SymTridiagonal{T<:Real}(dv::Vector{T}, ev::Vector{T})
SymTridiagonal{Float64}(float64(dv),float64(ev))
end
function SymTridiagonal{Td<:Number,Te<:Number}(dv::Vector{Td}, ev::Vector{Te})
T = promote(Td,Te)
SymTridiagonal(convert(Vector{T}, dv), convert(Vector{T}, ev))
end
copy(S::SymTridiagonal) = SymTridiagonal(S.dv,S.ev)
function full(S::SymTridiagonal)
M = diagm(S.dv)
for i in 1:length(S.ev)
j = i + 1
M[i,j] = M[j,i] = S.ev[i]
end
M
end
function show(io, S::SymTridiagonal)
println(io, summary(S), ":")
print(io, "diag: ")
print_matrix(io, (S.dv)')
print(io, "\n sup: ")
print_matrix(io, (S.ev)')
end
size(m::SymTridiagonal) = (length(m.dv), length(m.dv))
size(m::SymTridiagonal,d::Integer) = d<1 ? error("dimension out of range") : (d<2 ? length(m.dv) : 1)
eig(m::SymTridiagonal, vecs::Bool) = LAPACK.stev!(vecs ? 'V' : 'N', copy(m.dv), copy(m.ev))
eig(m::SymTridiagonal) = eig(m::SymTridiagonal, true)
## This function has been in Julia for some time. Could probably be dropped.
trideig{T<:BlasFloat}(d::Vector{T}, e::Vector{T}) = LAPACK.stev!('N', copy(d), copy(e))[1]
## Tridiagonal matrices ##
type Tridiagonal{T} <: AbstractMatrix{T}
dl::Vector{T} # sub-diagonal
d::Vector{T} # diagonal
du::Vector{T} # sup-diagonal
dutmp::Vector{T} # scratch space for vector RHS solver, sup-diagonal
rhstmp::Vector{T}# scratch space, rhs
function Tridiagonal(N::Integer)
dutmp = Array(T, N-1)
rhstmp = Array(T, N)
new(dutmp, rhstmp, dutmp, dutmp, rhstmp) # first three will be overwritten
end
end
function Tridiagonal{T<:Number}(dl::Vector{T}, d::Vector{T}, du::Vector{T})
N = length(d)
if length(dl) != N-1 || length(du) != N-1
error("The sub- and super-diagonals must have length N-1")
end
M = Tridiagonal{T}(N)
M.dl = copy(dl)
M.d = copy(d)
M.du = copy(du)
return M
end
function Tridiagonal{Tl<:Number, Td<:Number, Tu<:Number}(dl::Vector{Tl}, d::Vector{Td}, du::Vector{Tu})
R = promote(Tl, Td, Tu)
Tridiagonal(convert(Vector{R}, dl), convert(Vector{R}, d), convert(Vector{R}, du))
end
size(M::Tridiagonal) = (length(M.d), length(M.d))
function show(io, M::Tridiagonal)
println(io, summary(M), ":")
print(io, " sub: ")
print_matrix(io, (M.dl)')
print(io, "\ndiag: ")
print_matrix(io, (M.d)')
print(io, "\n sup: ")
print_matrix(io, (M.du)')
end
full{T}(M::Tridiagonal{T}) = convert(Matrix{T}, M)
function convert{T}(::Type{Matrix{T}}, M::Tridiagonal{T})
A = zeros(T, size(M))
for i = 1:length(M.d)
A[i,i] = M.d[i]
end
for i = 1:length(M.d)-1
A[i+1,i] = M.dl[i]
A[i,i+1] = M.du[i]
end
return A
end
function similar(M::Tridiagonal, T, dims::Dims)
if length(dims) != 2 || dims[1] != dims[2]
error("Tridiagonal matrices must be square")
end
return Tridiagonal{T}(dims[1])
end
copy(M::Tridiagonal) = Tridiagonal(M.dl, M.d, M.du)
# Operations on Tridiagonal matrices
round(M::Tridiagonal) = Tridiagonal(round(M.dl), round(M.d), round(M.du))
iround(M::Tridiagonal) = Tridiagonal(iround(M.dl), iround(M.d), iround(M.du))
## Solvers
#### Tridiagonal matrix routines ####
function \{T<:BlasFloat}(M::Tridiagonal{T}, rhs::StridedVecOrMat{T})
if stride(rhs, 1) == 1
return LAPACK.gtsv!(copy(M.dl), copy(M.d), copy(M.du), copy(rhs))
end
solve(M, rhs) # use the Julia "fallback"
end
# This is definitely not going to work
#eig(M::Tridiagonal) = LAPACK.stev!('V', copy(M))
# Allocation-free variants
# Note that solve is non-aliasing, so you can use the same array for
# input and output
function solve(x::AbstractArray, xrng::Ranges{Int}, M::Tridiagonal, rhs::AbstractArray, rhsrng::Ranges{Int})
d = M.d
N = length(d)
if length(xrng) != N || length(rhsrng) != N
error("dimension mismatch")
end
dl = M.dl
du = M.du
dutmp = M.dutmp
rhstmp = M.rhstmp
xstart = first(xrng)
xstride = step(xrng)
rhsstart = first(rhsrng)
rhsstride = step(rhsrng)
# Forward sweep
denom = d[1]
dulast = du[1] / denom
dutmp[1] = dulast
rhslast = rhs[rhsstart] / denom
rhstmp[1] = rhslast
irhs = rhsstart+rhsstride
for i in 2:N-1
dltmp = dl[i-1]