Merge pull request #16 from mbauman/sortedvector

Add a SortedVector for keyed axis indexes and hierarchical indexing

Author: tshort

src/AxisArrays.jl

@@ -7,6 +7,7 @@ export AxisArray, Axis, Interval, axisnames, axisvalues, axisdim, axes
 include("core.jl")
 include("intervals.jl")
 include("indexing.jl")
+include("sortedvector.jl")
 include("utils.jl")
 
 end

src/core.jl

@@ -291,7 +291,7 @@ checkaxis(ax) = checkaxis(axistrait(ax), ax)
 checkaxis(::Type{Unsupported}, ax) = nothing # TODO: warn or error?
 # Dimensional axes must be monotonically increasing
 checkaxis{T}(::Type{Dimensional}, ax::Range{T}) = step(ax) > zero(T) || error("Dimensional axes must be monotonically increasing")
-checkaxis(::Type{Dimensional}, ax) = issorted(ax, lt=(<=)) || error("Dimensional axes must be monotonically increasing")
+checkaxis(::Type{Dimensional}, ax) = issorted(ax) || error("Dimensional axes must be monotonically increasing")
 # Categorical axes must simply be unique
 function checkaxis(::Type{Categorical}, ax)
     seen = Set{eltype(ax)}()

src/indexing.jl

@@ -78,6 +78,8 @@ axisindexes(ax, idx) = axisindexes(axistrait(ax.val), ax.val, idx)
 axisindexes(::Type{Unsupported}, ax, idx) = error("elementwise indexing is not supported for axes of type $(typeof(ax))")
 # Dimensional axes may be indexed by intervals of their elements
 axisindexes{T}(::Type{Dimensional}, ax::AbstractVector{T}, idx::Interval{T}) = searchsorted(ax, idx)
+# Dimensional axes may also be indexed directy by their elements
+axisindexes{T}(::Type{Dimensional}, ax::AbstractVector{T}, idx::T) = searchsorted(ax, Interval(idx,idx))
 # Categorical axes may be indexed by their elements
 function axisindexes{T}(::Type{Categorical}, ax::AbstractVector{T}, idx::T)
     i = findfirst(ax, idx)

src/sortedvector.jl

@@ -0,0 +1,100 @@
+
+export SortedVector
+
+@doc """
+
+A SortedVector is an AbstractVector where the underlying data is
+ordered (monotonically increasing).
+
+Indexing that would unsort the data is prohibited. A SortedVector is a
+Dimensional axis, and no checking is done to ensure that the data is
+sorted. Duplicate values are allowed.
+
+A SortedVector axis can be indexed with an Interval, with a value, or
+with a vector of values. Use of a SortedVector{Tuple} axis allows
+indexing similar to the hierarchical index of the Python Pandas
+package or the R data.table package.
+
+### Constructors
+
+```julia
+SortedVector(x::AbstractVector)
+```
+
+### Keyword Arguments
+
+* `x::AbstractVector` : the wrapped vector
+
+### Examples
+
+```julia
+v = SortedVector(collect([1.; 10.; 10:15.]))
+A = AxisArray(reshape(1:16, 8, 2), v, [:a, :b])
+A[Interval(8.,12.), :]
+A[1., :]
+A[10., :]
+
+## Hierarchical index example with three key levels
+
+data = reshape(1.:40., 20, 2)
+v = collect(zip([:a, :b, :c][rand(1:3,20)], [:x,:y][rand(1:2,20)], [:x,:y][rand(1:2,20)]))
+idx = sortperm(v)
+A = AxisArray(data[idx,:], SortedVector(v[idx]), [:a, :b])
+A[:b, :]
+A[[:a,:c], :]
+A[(:a,:x), :]
+A[(:a,:x,:x), :]
+A[Interval(:a,:b), :]
+A[Interval((:a,:x),(:b,:x)), :]
+```
+
+""" ->
+immutable SortedVector{T} <: AbstractVector{T}
+    data::AbstractVector{T}
+end
+
+Base.getindex(v::SortedVector, idx::Int) = v.data[idx]
+Base.getindex(v::SortedVector, idx::Range1) = SortedVector(v.data[idx])
+Base.getindex(v::SortedVector, idx::StepRange) =
+    step(idx) > 0 ? SortedVector(v.data[idx]) : error("step must be positive to index a SortedVector")
+Base.getindex(v::SortedVector, idx::AbstractVector) =
+    issorted(idx) ? SortedVector(v.data[idx]) : error("index must be monotonically increasing to index a SortedVector")
+
+Base.length(v::SortedVector) = length(v.data)
+Base.size(v::SortedVector) = size(v.data)
+Base.size(v::SortedVector, i) = size(v.data, i)
+
+axistrait(::SortedVector) = Dimensional
+checkaxis(::SortedVector) = nothing
+
+
+## Add some special indexing for SortedVector{Tuple}'s to achieve something like
+## Panda's hierarchical indexing
+
+axisindexes{T<:Tuple,S}(ax::Axis{S,SortedVector{T}}, idx) =
+    searchsorted(ax.val, idx, 1, length(ax.val), Base.ord(_isless,identity,false,Base.Forward))
+
+axisindexes{T<:Tuple,S}(ax::Axis{S,SortedVector{T}}, idx::AbstractArray) =
+    vcat([axisindexes(ax, i) for i in idx]...)
+
+
+## Use a modification of `isless`, so that (:a,) is not less than (:a, :b).
+## This allows for more natural indexing.
+
+_isless(x,y) = isless(x,y)
+
+function _isless(t1::Tuple, t2::Tuple)
+    n1, n2 = length(t1), length(t2)
+    for i = 1:min(n1, n2)
+        a, b = t1[i], t2[i]
+        if !isequal(a, b)
+            return _isless(a, b)
+        end
+    end
+    return false
+end
+_isless{T<:Tuple}(t1::Interval{T}, t2::Tuple) = _isless(t1, Interval(t2,t2))
+_isless{T<:Tuple}(t1::Tuple, t2::Interval{T}) = _isless(Interval(t1,t1), t2)
+_isless(t1::Tuple, t2) = _isless(t1,(t2,))
+_isless(t1, t2::Tuple) = _isless((t1,),t2)
+_isless(a::Interval, b::Interval) = _isless(a.hi, b.lo)

test/runtests.jl

@@ -3,3 +3,4 @@ using Base.Test
 
 include("core.jl")
 include("indexing.jl")
+include("sortedvector.jl")

test/sortedvector.jl

@@ -0,0 +1,21 @@
+
+# Test SortedVector
+v = SortedVector(collect([1.; 10.; 10:15.]))
+A = AxisArray(reshape(1:16, 8, 2), v, [:a, :b])
+@test A[Interval(8.,12.), :] == A[2:5, :]
+@test A[1., :] == A[1, :]
+@test A[10., :] == A[2:3, :]
+
+# Test SortedVector with a hierarchical index (indexed using Tuples)
+srand(1234)
+data = reshape(1.:40., 20, 2)
+v = collect(zip([:a, :b, :c][rand(1:3,20)], [:x,:y][rand(1:2,20)], [:x,:y][rand(1:2,20)]))
+idx = sortperm(v)
+A = AxisArray(data[idx,:], SortedVector(v[idx]), [:a, :b])
+@test A[:b, :] == A[5:12, :]
+@test A[[:a,:c], :] == A[[1:4;13:end], :]
+@test A[(:a,:y), :] == A[2:4, :]
+@test A[(:c,:y,:y), :] == A[16:end, :]
+@test A[Interval(:a,:b), :] == A[1:12, :]
+@test A[Interval((:a,:x),(:b,:x)), :] ==  A[1:9, :]
+@test A[[Interval((:a,:x),(:b,:x)),:c], :] ==  A[[1:9;13:end], :]