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AxisArrays

Performant arrays where each dimension can have a named axis with values

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AxisArrays

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This package for the Julia language provides an array type (the AxisArray) that knows about its dimension names and axis values. This allows for indexing with the axis name without incurring any runtime overhead. AxisArrays can also be indexed by the values of their axes, allowing column names or interval selections. This permits one to implement algorithms that are oblivious to the storage order of the underlying arrays. In contrast to similar approaches in Images.jl and NamedArrays.jl, this allows for type-stable selection of dimensions and compile-time axis lookup. It is also better suited for regularly sampled axes, like samples over time.

Collaboration is welcome! This is still a work-in-progress. See the roadmap for the project's current direction.

Example of currently-implemented behavior:

julia> Pkg.clone("https://github.com/JuliaArrays/AxisArrays.jl")
       using AxisArrays, Unitful
       import Unitful: s, ms, µs

julia> fs = 40000 # Generate a 40kHz noisy signal, with spike-like stuff added for testing
       y = randn(60*fs+1)*3
       for spk = (sin.(0.8:0.2:8.6) .* [0:0.01:.1; .15:.1:.95; 1:-.05:.05]   .* 50,
                  sin.(0.8:0.4:8.6) .* [0:0.02:.1; .15:.1:1; 1:-.2:.1] .* 50)
           i = rand(round(Int,.001fs):1fs)
           while i+length(spk)-1 < length(y)
               y[i:i+length(spk)-1] += spk
               i += rand(round(Int,.001fs):1fs)
           end
       end

julia> A = AxisArray([y 2y], Axis{:time}(0s:1s/fs:60s), Axis{:chan}([:c1, :c2]))
2-dimensional AxisArray{Float64,2,...} with axes:
    :time, 0.0 s:2.5e-5 s:60.0 s
    :chan, [:c1,:c2]
And data, a 2400001x2 Array{Float64,2}:
 -3.06091    -6.12181
  0.152334    0.304668
  7.86831    15.7366
 -1.4144     -2.82879
 -2.02881    -4.05763
  9.87901    19.758
  ⋮
 -0.0254444  -0.0508888
  0.204358    0.408717
 -4.80093    -9.60186
  5.39751    10.795
  0.976276    1.95255
  0.336558    0.673116

AxisArrays behave like regular arrays, but they additionally use the axis information to enable all sorts of fancy behaviors. For example, we can specify indices in any order, just so long as we annotate them with the axis name:

julia> A[Axis{:time}(4)]
2-dimensional AxisArray{Float64,1,...} with axes:
    :chan, Symbol[:c1,:c2]
And data, a 2-element Array{Float64,1}:
 -1.4144  -2.82879

julia> A[Axis{:chan}(:c2), Axis{:time}(1:5)]
1-dimensional AxisArray{Float64,1,...} with axes:
    :time, 0.0 s:2.5e-5 s:0.0001 s
A[Axis{:chan}(:c2), Axis{:time}(1:5)]:
 -6.12181
  0.304668
 15.7366
 -2.82879
 -4.05763

We can also index by the values of each axis using an Interval type that selects all values between two endpoints a .. b or the axis values directly. Notice that the returned AxisArray still has axis information itself... and it still has the correct time information for those datapoints!

julia> A[40µs .. 220µs, :c1]
1-dimensional AxisArray{Float64,1,...} with axes:
    :time, 5.0e-5 s:2.5e-5 s:0.0002 s
And data, a 7-element Array{Float64,1}:
  7.86831
 -1.4144
 -2.02881
  9.87901
  0.463201
  2.49211
 -1.97716

julia> axes(ans, 1)
AxisArrays.Axis{:time,StepRangeLen{Quantity{Float64, Dimensions:{𝐓}, Units:{s}},Base.TwicePrecision{Quantity{Float64, Dimensions:{𝐓}, Units:{s}}},Base.TwicePrecision{Quantity{Float64, Dimensions:{𝐓}, Units:{s}}}}}(5.0e-5 s:2.5e-5 s:0.0002 s)

Sometimes, though, what we're really interested in is a window of time about a specific index. The operation above (looking for values in the window from 40µs to 220µs) might be more clearly expressed as a symmetrical window about a specific index where we know something interesting happened. To represent this, we use the atindex function:

julia> A[atindex(-90µs .. 90µs, 5), :c2]
1-dimensional AxisArray{Float64,1,...} with axes:
    :time_sub, -7.5e-5 s:2.5e-5 s:7.5e-5 s
And data, a 7-element SubArray{Float64,1,Array{Float64,2},Tuple{AxisArrays.AxisArray{Int64,1,UnitRange{Int64},Tuple{AxisArrays.Axis{:sub,SIUnits.SIRange{FloatRange{Float64},Float64,0,0,1,0,0,0,0,0,0}}}},Int64},0}:
 15.7366
 -2.82879
 -4.05763
 19.758
  0.926402
  4.98423
 -3.95433

Note that the returned AxisArray has its time axis shifted to represent the interval about the given index! This simple concept can be extended to some very powerful behaviors. For example, let's threshold our data and find windows about those threshold crossings.

julia> idxs = find(diff(A[:,:c1] .< -15) .> 0)
242-element Array{Int64,1}: ...

julia> spks = A[atindex(-200µs .. 800µs, idxs), :c1]
2-dimensional AxisArray{Float64,2,...} with axes:
    :time_sub, -0.000175 s:2.5e-5 s:0.000775 s
    :time_rep, Quantity{Float64, Dimensions:{𝐓}, Units:{s}}[0.178725 s,0.806825 s,0.88305 s,1.47485 s,1.50465 s,1.53805 s,1.541025 s,2.16365 s,2.368425 s,2.739 s  …  57.797925 s,57.924075 s,58.06075 s,58.215125 s,58.6403 s,58.96215 s,58.990225 s,59.001325 s,59.48395 s,59.611525 s]
And data, a 39x242 Array{Float64,2}:
 -1.53038     4.72882     5.8706    …  -0.231564      0.624714   3.44076
 -2.24961     2.12414     5.69936       7.00179       2.30993    5.20432
  5.96311     3.9713     -4.38335       1.32617      -0.686648   0.443454
  3.86592     5.7466      2.32469       1.30803       3.44585    1.17781
  3.56837    -3.32178     1.16106      -3.91796       2.41779   -6.17495
 -9.52063    -2.07014    -1.18463   …  -3.55719       2.23117    1.76089
  ⋮                                 ⋱                 ⋮
  3.51708    -1.63627     0.281915     -2.41759       3.39403    0.101004
  0.0421772  -2.13557    -4.71965       0.066912      3.25141   -0.445574
  3.53238    -3.72221     1.68314   …  -4.15147      -5.25241   -1.77557
 -4.38307     1.38275    -1.33641       3.40342       0.272826  -3.22013
  2.54846    -0.0194032   2.58679      -0.000676503  -2.71147   -0.288483
  0.260694   -4.1724     -0.111377      3.283         1.77147   -0.367888

By indexing with a repeated interval, we have added a dimension to the output! The returned AxisArray's columns specify each repetition of the interval, and each datapoint in the column represents a timepoint within that interval, adjusted by the time of the theshold crossing. The best part here is that the returned matrix knows precisely where its data came from, and has labeled its dimensions appropriately. Not only is there the proper time base for each waveform, but we also have recorded the event times as the axis across the columns.

Now we can do a cursory clustering analysis on these spike snippets to separate the two "neurons" back out into their own groups with Clustering.jl, and plot using Gadfly.

julia> using Clustering
       Ks = Clustering.kmeans(spks.data, 2);

julia> using Gadfly
       plot(spks, x=:time_sub, y=:data, group=:time_rep, color=DataFrames.RepeatedVector(Ks.assignments, size(spks, 1), 1), Geom.line)

clustered spike snippets

Indexing

Indexing axes

Two main types of Axes supported by default include:

  • Categorical axis -- These are vectors of labels, normally symbols or strings. Elements or slices can be selected by elements or vectors of elements.

  • Dimensional axis -- These are sorted vectors or iterators that can be selected by Intervals. These are commonly used for sequences of times or date-times. For regular sample rates, ranges can be used.

Here is an example with a Dimensional axis representing a time sequence along rows and a Categorical axis of symbols for column headers.

B = AxisArray(reshape(1:15, 5, 3), .1:.1:0.5, [:a, :b, :c])
B[Axis{:row}(Interval(.2,.4))] # restrict the AxisArray along the time axis
B[Interval(0.,.3), [:a, :c]]   # select an interval and two of the columns

User-defined axis types can be added along with custom indexing behaviors.

Example: compute the intensity-weighted mean along the z axis

B = AxisArray(randn(100,100,100), :x, :y, :z)
Itotal = sumz = 0.0
for iter in eachindex(B)  # traverses in storage order for cache efficiency
    I = B[iter]  # intensity in a single voxel
    Itotal += I
    sumz += I * iter[axisdim(B, Axis{:z})]  # axisdim "looks up" the z dimension
end
meanz = sumz/Itotal

The intention is that all of these operations are just as efficient as they would be if you used traditional position-based indexing with all the inherent assumptions about the storage order of B.

First Commit

02/13/2015

Last Touched

13 days ago

Commits

221 commits