Merge branch 'master' of https://github.com/JuliaStats/Distances.jl

Author: KristofferC

src/Distances.jl

@@ -58,7 +58,6 @@ export
     rogerstanimoto,
     chebyshev,
     minkowski,
-    mahalanobis,
 
     hamming,
     cosine_dist,

src/common.jl

@@ -64,7 +64,7 @@ function get_colwise_dims(d::Int, r::AbstractArray, a::AbstractVector, b::Abstra
 end
 
 function get_colwise_dims(d::Int, r::AbstractArray, a::AbstractMatrix, b::AbstractVector)
-    size(a, 1) == length(b) == d
+    size(a, 1) == length(b) == d ||
         throw(DimensionMismatch("Incorrect vector dimensions."))
     length(r) == size(a, 2) || throw(DimensionMismatch("Incorrect size of r."))
     return size(a)
@@ -109,10 +109,10 @@ function sumsq_percol(a::AbstractMatrix{T}) where {T}
     return r
 end
 
-function wsumsq_percol(w::AbstractArray{T1}, a::AbstractMatrix{T2}) where {T1,T2}
+function wsumsq_percol(w::AbstractArray{T1}, a::AbstractMatrix{T2}) where {T1, T2}
     m = size(a, 1)
     n = size(a, 2)
-    T = typeof(one(T1)*one(T2))
+    T = typeof(one(T1) * one(T2))
     r = Vector{T}(n)
     for j = 1:n
         aj = view(a, :, j)
@@ -126,16 +126,16 @@ function wsumsq_percol(w::AbstractArray{T1}, a::AbstractMatrix{T2}) where {T1,T2
 end
 
 function dot_percol!(r::AbstractArray, a::AbstractMatrix, b::AbstractMatrix)
-    m = size(a,1)
-    n = size(a,2)
-    size(b) == (m,n) && length(r) == n ||
+    m = size(a, 1)
+    n = size(a, 2)
+    size(b) == (m, n) && length(r) == n ||
         throw(DimensionMismatch("Inconsistent array dimensions."))
     for j = 1:n
-        aj = view(a,:,j)
-        bj = view(b,:,j)
+        aj = view(a, :, j)
+        bj = view(b, :, j)
         r[j] = dot(aj, bj)
     end
     return r
 end
 
-dot_percol(a::AbstractMatrix, b::AbstractMatrix) = dot_percol!(Vector{Float64}(size(a,2)), a, b)
+dot_percol(a::AbstractMatrix, b::AbstractMatrix) = dot_percol!(Vector{Float64}(size(a, 2)), a, b)

src/generic.jl

@@ -32,7 +32,7 @@ result_type(::PreMetric, ::AbstractArray, ::AbstractArray) = Float64
 function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractVector, b::AbstractMatrix)
     n = size(b, 2)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
-    for j = 1 : n
+    for j = 1:n
         @inbounds r[j] = evaluate(metric, a, view(b, :, j))
     end
     r
@@ -41,7 +41,7 @@ end
 function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractMatrix, b::AbstractVector)
     n = size(a, 2)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
-    for j = 1 : n
+    for j = 1:n
         @inbounds r[j] = evaluate(metric, view(a, :, j), b)
     end
     r
@@ -50,7 +50,7 @@ end
 function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix)
     n = get_common_ncols(a, b)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
-    for j = 1 : n
+    for j = 1:n
         @inbounds r[j] = evaluate(metric, view(a, :, j), view(b, :, j))
     end
     r
@@ -85,10 +85,10 @@ function pairwise!(r::AbstractMatrix, metric::PreMetric, a::AbstractMatrix, b::A
     na = size(a, 2)
     nb = size(b, 2)
     size(r) == (na, nb) || throw(DimensionMismatch("Incorrect size of r."))
-    for j = 1 : size(b, 2)
-        bj = view(b,:,j)
-        for i = 1 : size(a, 2)
-            @inbounds r[i,j] = evaluate(metric, view(a,:,i), bj)
+    for j = 1:size(b, 2)
+        bj = view(b, :, j)
+        for i = 1:size(a, 2)
+            @inbounds r[i, j] = evaluate(metric, view(a, :, i), bj)
         end
     end
     r
@@ -101,14 +101,14 @@ end
 function pairwise!(r::AbstractMatrix, metric::SemiMetric, a::AbstractMatrix)
     n = size(a, 2)
     size(r) == (n, n) || throw(DimensionMismatch("Incorrect size of r."))
-    for j = 1 : n
-        aj = view(a,:,j)
-        for i = j+1 : n
-            @inbounds r[i,j] = evaluate(metric, view(a,:,i), aj)
+    for j = 1:n
+        aj = view(a, :, j)
+        for i = (j + 1):n
+            @inbounds r[i, j] = evaluate(metric, view(a, :, i), aj)
         end
-        @inbounds r[j,j] = 0
-        for i = 1 : j-1
-            @inbounds r[i,j] = r[j,i]   # leveraging the symmetry of SemiMetric
+        @inbounds r[j, j] = 0
+        for i = 1:(j - 1)
+            @inbounds r[i, j] = r[j, i]   # leveraging the symmetry of SemiMetric
         end
     end
     r

src/mahalanobis.jl

@@ -13,7 +13,7 @@ result_type(::SqMahalanobis{T}, ::AbstractArray, ::AbstractArray) where {T} = T
 
 # SqMahalanobis
 
-function evaluate(dist::SqMahalanobis{T}, a::AbstractVector, b::AbstractVector) where {T <: AbstractFloat}
+function evaluate(dist::SqMahalanobis{T}, a::AbstractVector, b::AbstractVector) where {T <: Real}
     if length(a) != length(b)
         throw(DimensionMismatch("first array has length $(length(a)) which does not match the length of the second, $(length(b))."))
     end
@@ -25,22 +25,22 @@ end
 
 sqmahalanobis(a::AbstractVector, b::AbstractVector, Q::AbstractMatrix) = evaluate(SqMahalanobis(Q), a, b)
 
-function colwise!(r::AbstractArray, dist::SqMahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: AbstractFloat}
+function colwise!(r::AbstractArray, dist::SqMahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: Real}
     Q = dist.qmat
     m, n = get_colwise_dims(size(Q, 1), r, a, b)
     z = a - b
     dot_percol!(r, Q * z, z)
 end
 
-function colwise!(r::AbstractArray, dist::SqMahalanobis{T}, a::AbstractVector, b::AbstractMatrix) where {T <: AbstractFloat}
+function colwise!(r::AbstractArray, dist::SqMahalanobis{T}, a::AbstractVector, b::AbstractMatrix) where {T <: Real}
     Q = dist.qmat
     m, n = get_colwise_dims(size(Q, 1), r, a, b)
     z = a .- b
     Qz = Q * z
     dot_percol!(r, Q * z, z)
 end
 
-function pairwise!(r::AbstractMatrix, dist::SqMahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: AbstractFloat}
+function pairwise!(r::AbstractMatrix, dist::SqMahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: Real}
     Q = dist.qmat
     m, na, nb = get_pairwise_dims(size(Q, 1), r, a, b)
 
@@ -50,29 +50,29 @@ function pairwise!(r::AbstractMatrix, dist::SqMahalanobis{T}, a::AbstractMatrix,
     sb2 = dot_percol(b, Qb)
     At_mul_B!(r, a, Qb)
 
-    for j = 1 : nb
-        @simd for i = 1 : na
-            @inbounds r[i,j] = sa2[i] + sb2[j] - 2 * r[i,j]
+    for j = 1:nb
+        @simd for i = 1:na
+            @inbounds r[i, j] = sa2[i] + sb2[j] - 2 * r[i, j]
         end
     end
     r
 end
 
-function pairwise!(r::AbstractMatrix, dist::SqMahalanobis{T}, a::AbstractMatrix) where {T <: AbstractFloat}
+function pairwise!(r::AbstractMatrix, dist::SqMahalanobis{T}, a::AbstractMatrix) where {T <: Real}
     Q = dist.qmat
     m, n = get_pairwise_dims(size(Q, 1), r, a)
 
     Qa = Q * a
     sa2 = dot_percol(a, Qa)
     At_mul_B!(r, a, Qa)
 
-    for j = 1 : n
-        for i = 1 : j-1
-            @inbounds r[i,j] = r[j,i]
+    for j = 1:n
+        for i = 1:(j - 1)
+            @inbounds r[i, j] = r[j, i]
         end
-        r[j,j] = 0
-        for i = j+1 : n
-            @inbounds r[i,j] = sa2[i] + sa2[j] - 2 * r[i,j]
+        r[j, j] = 0
+        for i = (j + 1):n
+            @inbounds r[i, j] = sa2[i] + sa2[j] - 2 * r[i, j]
         end
     end
     r
@@ -81,24 +81,24 @@ end
 
 # Mahalanobis
 
-function evaluate(dist::Mahalanobis{T}, a::AbstractVector, b::AbstractVector) where {T <: AbstractFloat}
+function evaluate(dist::Mahalanobis{T}, a::AbstractVector, b::AbstractVector) where {T <: Real}
     sqrt(evaluate(SqMahalanobis(dist.qmat), a, b))
 end
 
 mahalanobis(a::AbstractVector, b::AbstractVector, Q::AbstractMatrix) = evaluate(Mahalanobis(Q), a, b)
 
-function colwise!(r::AbstractArray, dist::Mahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: AbstractFloat}
+function colwise!(r::AbstractArray, dist::Mahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: Real}
     sqrt!(colwise!(r, SqMahalanobis(dist.qmat), a, b))
 end
 
-function colwise!(r::AbstractArray, dist::Mahalanobis{T}, a::AbstractVector, b::AbstractMatrix) where {T <: AbstractFloat}
+function colwise!(r::AbstractArray, dist::Mahalanobis{T}, a::AbstractVector, b::AbstractMatrix) where {T <: Real}
     sqrt!(colwise!(r, SqMahalanobis(dist.qmat), a, b))
 end
 
-function pairwise!(r::AbstractMatrix, dist::Mahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: AbstractFloat}
+function pairwise!(r::AbstractMatrix, dist::Mahalanobis{T}, a::AbstractMatrix, b::AbstractMatrix) where {T <: Real}
     sqrt!(pairwise!(r, SqMahalanobis(dist.qmat), a, b))
 end
 
-function pairwise!(r::AbstractMatrix, dist::Mahalanobis{T}, a::AbstractMatrix) where {T <: AbstractFloat}
+function pairwise!(r::AbstractMatrix, dist::Mahalanobis{T}, a::AbstractMatrix) where {T <: Real}
     sqrt!(pairwise!(r, SqMahalanobis(dist.qmat), a))
 end