This packages provides Julia arrays with named dimensions. Like the built-in Array type these are mutable objects, unlike NamedArrays and AxisArrays which are immutable.
The idea was to have a convenient way to gather results of calculations in a script or notebook, rather than for anything high-performance.
For example, here I have a matrix of results at each iteration, and nest
these into a 3-tensor, whose axis order I need not remember:
using DimArrays
list = [];
for i=1:33
slowcalc = sqrt(i) .* randn(3,13) .+ i
push!(list, DimArray(slowcalc, :a, :b, :c )) # add labels for 1st and 2nd dimensions
end
list3 = nest(list, :iter) # now i is the 3rd index, and named "iter"
using Statistics
mean(list3, dims=:iter) # equivalent to dropdims(mean(list3, dims=3), dims=3)
For quick plots, dimension names are used for axes and series:
using Plots
plot(selectdim(list3, :b, 1)' , legend=:bottomright)
Here selectdim(list3, :b, 1) == list3[:,1,:]
in contents, but retains the labels.
Besides each dimension's name (which is a Symbol, strings will be converted) it can also store a function, which is used in plotting to scale the axes etc.
(But only the output, getindex
uses original integer indices).
You can pass a number by which to scale the index, or a dictionary, instead of a function.
For example, this plots data saved every 4 iterations correctly over the above example:
saveevery = 4
list4 = DimArray([], :iter, saveevery); # equivalent to function i->4i
for i=1:33
slowcalc = sqrt(i) .* randn(3,23) .+ i
slownice = DimArray(slowcalc, [:a, :b], [Dict(1=>"one", 2=>"two", 3=>"three")], :stuff )
# equivalent to i->Dict(...)[i]
rem(i,saveevery)==0 && push!(list4, slownice)
end
nest(list4)
plot!(mean(nest(list4), dims=:b)', s=:dash)
If you do not provide a name for a dimension (or give an empty string "")
then you can still refer to it by default names like size(x, :row) == size(x,1)
or maximum(y, :col)
etc.
However these defaults are not stored, and not manipulated by transpose(x)
or kron(x,y)
.
For now, the list of functions supported is:
DimArray
, DimVector
, DimMatrix
create one, taking names and functions for dimensions in the order given.dictvector
defines a DimVector whose function is a Dict. nest
converts arrays of arrays, and squeeze
drops dimensions of size 1. and these built-in functions:
selectdim, size
understand a dimension's name.sum, maximum, minimum, dropdims
and Statistics.mean, std
: all can be called with a dimension's name, in which case by default squeeze=true
on that dimension, like mean(..., dims=:b)
above.
They can also be called with a list of dimensions: sum(x, dims=[1,:c])
etc.push!, append!, hcat, vcat, transpose, ctranspose, permutedims
.*
will warn (once) if you multiply along directions with mismatched names... which may be a terrible idea.
And kron
ecker products produce new names like :a_b
.collect
, implicitly used by comprehensions like [ sqrt(n) for n in DimVector(1:10, "int")' ]
which thus inherit the names of the array being iterated over.Since DimArray <: AbstractArray
anything else will fall back on their methods, and forget the dimension labels.
See also:
ToDo:
x[:, 1:10:end]
and hcat(a,b)
update the functions correctly.Michael Abbott, January 2018, mostly (as I had a grant to write).
07/21/2018
over 2 years ago
6 commits