Extending Base.stack for DimArrays #645

brendanjohnharris · 2024-02-23T06:29:57Z

Adds methods for Base.stack, and related non-exported functions from Base, that are compatible with DimArrays.

Syntax follows Base: stacking DimArrays along a given axis dims creates a new dimension. However, existing dimension data is preserved, and the new dimension becomes an AnonDim.

Optionally, a Dimension dim can be provided as the first argument to stack, in which case the new dimension is assigned as dim rather than AnonDim.

codecov-commenter · 2024-02-23T06:43:09Z

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@@            Coverage Diff             @@
##             main     #645      +/-   ##
==========================================
+ Coverage   83.83%   83.99%   +0.15%     
==========================================
  Files          45       45              
  Lines        4102     4136      +34     
==========================================
+ Hits         3439     3474      +35     
+ Misses        663      662       -1

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rafaqz · 2024-02-23T09:03:13Z

src/array/methods.jl

@@ -131,15 +131,15 @@ end
    """
    function Base.eachslice(A::AbstractDimArray; dims)
        dimtuple = _astuple(dims)
-        if !(dimtuple == ()) 
+        if !(dimtuple == ())


Would be nice to remove all these whitespace changes so we can see the real changes

rafaqz · 2024-02-23T09:06:25Z

src/array/methods.jl

+    end
+
+    newdims = first(origdims)
+    newdims = ntuple(d -> d == newdim ? AnonDim() : newdims[d-(d>newdim)], length(newdims) + 1)


maybe make this a do block so its easier to read

rafaqz · 2024-02-23T09:08:11Z

src/array/methods.jl


 To fix for `AbstractDimArray`, pass new lookup values as `cat(As...; dims=$D(newlookupvals))` keyword or `dims=$D()` for empty `NoLookup`.
 """

+function Base._typed_stack(::Colon, ::Type{T}, ::Type{S}, A, Aax=_iterator_axes(A)) where {T,S<:AbstractDimArray}
+    origdims = dims.(A)


Suggested change

origdims = dims.(A)

origdims = map(dims, A)

rafaqz · 2024-02-23T09:10:56Z

src/array/methods.jl

+    DimArray(_A, newdims)
+end
+
+function Base.stack(dim::Dimension, A::AbstractVector{<:AbstractDimArray}; dims=nothing, kwargs...)


Whats the idea with dim as the first argument?

The tests also don't hit this code.

brendanjohnharris · 2024-02-27T05:00:45Z

Thanks for the suggestions! Went through and cleaned up the PR.

The Base.stack(dim, X; dims) method lets you supply a Dimension to assign to the newly created array dimension; not strictly necessary, but more convenient than setting or rebuilding the resulting array to overwrite the new AnonDim (is an AnonDim a suitable way to treat a newly created dimension, as I've done here?).

Let me know if you have more thoughts on this, happy to work on it further :)

rafaqz · 2024-02-27T07:24:27Z

src/array/methods.jl

+true
+```
+"""
+function Base.stack(dim::Dimension, A::AbstractVector{<:AbstractDimArray}; dims=nothing, kwargs...)


Why not pass dim in dims?

This method signature is a bit strange , we usually try not to add varients on Base methods, we just allow dims to specify named dimensions.

rafaqz · 2024-02-27T07:32:43Z

We try not to change base method signatures besides allowing dims to be named. To keep the mental model very simple.

I would just put that new Dimension in dims like cat does. If its a constructed dimension it replaces the existing one. Otherwise Type/Symbol etc just choose them. Just check d isa Dimension

You will also need to format(newdims, A) afterwards.

brendanjohnharris · 2024-02-28T03:08:54Z

Base.stack behaves differently than Base.cat in that it always creates a new dimension (i.e. Base.stack([A, B,...]; dims=2) inserts a dimension at position 2, increasing ndims(A) by 1); in general this new dimension is unrelated to the existing array dimensions, so we need to specify both position (dims) and a Dimension (dim).

I see your point about keeping new signatures to a minimum, though. How about allowing the keyword argument dims to be assigned as an 'Integer=>Dimension' pair, with the following behavior:

If dims isa Integer: The new dimension is an AnonDim at position dims
If dims isa Dimension: The new dimension is a DImension dims at position ndims(A)+1
If dims isa Pair{Integer, Dimension}: The new dimension is a Dimension last(dims) at position first(dims)

We could also, instead, have that the new dimension is always an AnonDim, leaving it up to the user to set that dimension at a later time; in that case, however, there is ambiguity if there are any existing AnonDims in the input arrays.

rafaqz · 2024-02-28T21:21:45Z

Using a Pair sounds like a good solution (as do points 1 and 2 as simpler cases). For 2 I guess putting it as the last dimension would be the majority use-case? (I rarely use stack)

Always AnonDim will require using set all the time with AnonDim => somedim. We may as well just put that pair in stack and skip the step.

rafaqz · 2024-03-03T12:13:45Z

src/array/methods.jl

+true
+```
+"""
+function Base.stack(A::AbstractVector{<:AbstractDimArray}; dims=Pair(ndims(A[1]), AnonDim()), kwargs...)


Suggested change

function Base.stack(A::AbstractVector{<:AbstractDimArray}; dims=Pair(ndims(A[1]), AnonDim()), kwargs...)

function Base.stack(A::AbstractVector{<:AbstractDimArray}; dims=Pair(ndims(A[1]) + 1, AnonDim()), kwargs...)

Isn't the default ndims(A) + 1 ?

rafaqz · 2024-03-03T12:16:53Z

src/array/methods.jl

+    dims isa Integer && (dims = dims => AnonDim())
+    dims isa Dimension && (dims = ndims(A[1])+1 => dims)


Suggested change

dims isa Integer && (dims = dims => AnonDim())

dims isa Dimension && (dims = ndims(A[1])+1 => dims)

if dims isa Integer

dims = dims => AnonDim())

elseif dims isa Dimension

dims = ndims(A[1])+1 => dims)

end

Assigning after && is best avoided as the assignment is hard to see when skimming code

rafaqz · 2024-03-03T12:24:26Z

src/array/methods.jl

+        end
+        newdims = format(newdims, B)
+
+        B = rebuild(B; dims=newdims)


Suggested change

B = rebuild(B; dims=newdims)

B = rebuild(B; dims=format(newdims, B))

User specified dims are usually incomplete and possibly incorrect

rafaqz · 2024-03-09T21:10:51Z

src/array/methods.jl

@@ -547,6 +547,100 @@ $message on dimension $D.
 To fix for `AbstractDimArray`, pass new lookup values as `cat(As...; dims=$D(newlookupvals))` keyword or `dims=$D()` for empty `NoLookup`.
 """

+function Base._typed_stack(::Colon, ::Type{T}, ::Type{S}, A, Aax=_iterator_axes(A)) where {T,S<:AbstractDimArray}


How stable do you think these methods are... could we add a method to Base.stack instead? What do we gain from touching these internals?

I know we use internals elsewhere, but we should stop:
#522

rafaqz · 2024-03-09T21:13:22Z

src/array/methods.jl

+    end
+
+    newdims = first(origdims)
+    newdims = ntuple(length(newdims) + 1) do d


Is this type-stable?

src/array/methods.jl

brendanjohnharris added 2 commits February 23, 2024 17:27

Extend Base.stack to DimArrays

4ea5e40

Initial Base.stack tests

ec3b2cf

brendanjohnharris mentioned this pull request Feb 23, 2024

Piracy! brendanjohnharris/TimeseriesTools.jl#10

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brendanjohnharris added 4 commits February 24, 2024 00:01

Fix whitespace changes

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Merge branch 'stack' into stacker

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Clean up Base.stack, add docstrings, add tests

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Fix Base.stack docstring

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brendanjohnharris marked this pull request as ready for review February 27, 2024 05:01

rafaqz reviewed Feb 27, 2024

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New Pair syntax for extended Base.stack

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brendanjohnharris and others added 3 commits March 7, 2024 14:31

Better Base.stack formatting

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Tweak docstring for Base.stack, remove kwargs

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Merge branch 'rafaqz:main' into stack

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brendanjohnharris force-pushed the stack branch 2 times, most recently from a93d665 to 7a4cf26 Compare March 7, 2024 05:01

brendanjohnharris added 3 commits March 7, 2024 16:10

Update whitespace

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Fix whitespace

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src/array/methods.jl

end

newdims = first(origdims)

newdims = ntuple(length(newdims) + 1) do d

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Is this type-stable?

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use rebuild

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Extending Base.stack for DimArrays #645

Extending Base.stack for DimArrays #645

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rafaqz Mar 9, 2024

	function Base.stack(A::AbstractVector{<:AbstractDimArray}; dims=Pair(ndims(A[1]), AnonDim()), kwargs...)
	function Base.stack(A::AbstractVector{<:AbstractDimArray}; dims=Pair(ndims(A[1]) + 1, AnonDim()), kwargs...)

		dims isa Integer && (dims = dims => AnonDim())
		dims isa Dimension && (dims = ndims(A[1])+1 => dims)

	B = rebuild(B; dims=newdims)
	B = rebuild(B; dims=format(newdims, B))

Extending Base.stack for DimArrays #645

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Extending Base.stack for DimArrays #645

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