Overhaul DimTable (#536)

* Add initial implementation of `mergedims`

* Use values instead of layers

* Simplify base method

* Perform all checks in main method

* Simplify mergedims for arrays

* Handle case where different numbers of dims provided

* Add mergedims to docs

* Implemented WideDimTable

* Removed Dead Code

* mergedims now allows selection of specific dimensions

* Dropped MergedDimColumn

* cleaned up code

* More cleanup

* Added comparedims when constructing a DimTable from multiple AbstractDimArrays

* mergedims can now accept dimensions that are not present in the stack/array

* Implemented unmergedims

* Removed unnecessary argument from undergedims

* DimTable now preserves name of AbstractDimArray if present.

* Added parent field to DimTable

* Passed test cases

* Added test cases and updated docs

* Updated docs for DimTable

* Updated docs and test cases

* Removed Any[]

---------

Co-authored-by: Seth Axen <[email protected]>

docs/src/reference.md

@@ -50,6 +50,8 @@ rebuild
 modify
 broadcast_dims
 broadcast_dims!
+mergedims
+unmergedims
 reorder
 Base.cat
 Base.map

src/DimensionalData.jl

@@ -66,7 +66,7 @@ export dims, refdims, metadata, name, lookup, bounds
 export dimnum, hasdim, hasselection, otherdims
 
 # utils
-export set, rebuild, reorder, modify, broadcast_dims, broadcast_dims!
+export set, rebuild, reorder, modify, broadcast_dims, broadcast_dims!, mergedims, unmergedims
 
 const DD = DimensionalData
 

src/Dimensions/primitives.jl

@@ -12,6 +12,7 @@ or are at least rotations/transformations of the same type.
 """
 @inline dimsmatch(dims, query) = dimsmatch(<:, dims, query)
 @inline function dimsmatch(f::Function, dims::Tuple, query::Tuple)
+    length(dims) == length(query) || return false
     all(map((d, l) -> dimsmatch(f, d, l), dims, query))
 end
 @inline dimsmatch(f::Function, dim, query) = dimsmatch(f, typeof(dim), typeof(query))

src/array/array.jl

@@ -576,3 +576,120 @@ end
 # Thed default constructor is DimArray
 dimconstructor(dims::DimTuple) = dimconstructor(tail(dims)) 
 dimconstructor(dims::Tuple{}) = DimArray 
+
+"""
+    mergedims(old_dims => new_dim) => Dimension
+
+Return a dimension `new_dim` whose indices are a [`MergedLookup`](@ref) of the indices of
+`old_dims`.
+"""
+function mergedims((old_dims, new_dim)::Pair)
+    data = vec(DimPoints(_astuple(old_dims)))
+    return rebuild(basedims(new_dim), MergedLookup(data, old_dims))
+end
+
+"""
+    mergedims(dims, old_dims => new_dim, others::Pair...) => dims_new
+
+If dimensions `old_dims`, `new_dim`, etc. are found in `dims`, then return new `dims_new`
+where all dims in `old_dims` have been combined into a single dim `new_dim`.
+The returned dimension will keep only the name of `new_dim`. Its coords will be a
+[`MergedLookup`](@ref) of the coords of the dims in `old_dims`. New dimensions are always
+placed at the end of `dims_new`. `others` contains other dimension pairs to be merged.
+
+# Example
+````jldoctest
+julia> ds = (X(0:0.1:0.4), Y(10:10:100), Ti([0, 3, 4]));
+julia> mergedims(ds, Ti => :time, (X, Y) => :space)
+Dim{:time} MergedLookup{Tuple{Int64}} Tuple{Int64}[(0,), (3,), (4,)] Ti,
+Dim{:space} MergedLookup{Tuple{Float64, Int64}} Tuple{Float64, Int64}[(0.0, 10), (0.1, 10), …, (0.3, 100), (0.4, 100)] X, Y
+````
+"""
+function mergedims(all_dims, dim_pairs::Pair...)
+    # filter out dims completely missing
+    dim_pairs = map(x -> _filter_dims(all_dims, first(x)) => last(x), dim_pairs)
+    dim_pairs_complete = filter(dim_pairs) do (old_dims,)
+        dims_present = dims(all_dims, _astuple(old_dims))
+        isempty(dims_present) && return false
+        all(hasdim(dims_present, old_dims)) || throw(ArgumentError(
+            "Not all dimensions $old_dims found in $(map(basetypeof, all_dims))"
+        ))
+        return true
+    end
+    isempty(dim_pairs_complete) && return all_dims
+    dim_pairs_concrete = map(dim_pairs_complete) do (old_dims, new_dim)
+        return dims(all_dims, _astuple(old_dims)) => new_dim
+    end
+    # throw error if old dim groups overlap
+    old_dims_tuples = map(first, dim_pairs_concrete)
+    if !dimsmatch(_cat_tuples(old_dims_tuples...), combinedims(old_dims_tuples...))
+        throw(ArgumentError("Dimensions to be merged are not all unique"))
+    end
+    return _mergedims(all_dims, dim_pairs_concrete...)
+end
+
+"""
+    mergedims(A::AbstractDimArray, dim_pairs::Pair...) => AbstractDimArray
+    mergedims(A::AbstractDimStack, dim_pairs::Pair...) => AbstractDimStack
+
+Return a new array or stack whose dimensions are the result of [`mergedims(dims(A), dim_pairs)`](@ref).
+"""
+function mergedims(A::AbstractDimArray, dim_pairs::Pair...)
+    isempty(dim_pairs) && return A
+    all_dims = dims(A)
+    dims_new = mergedims(all_dims, dim_pairs...)
+    dimsmatch(all_dims, dims_new) && return A
+    dims_perm = _unmergedims(dims_new, map(last, dim_pairs))
+    Aperm = PermutedDimsArray(A, dims_perm)
+    data_merged = reshape(data(Aperm), map(length, dims_new))
+    rebuild(A, data_merged, dims_new)
+end
+
+"""
+    unmergedims(merged_dims::Tuple{Vararg{Dimension}}) => Tuple{Vararg{Dimension}}
+
+Return the unmerged dimensions from a tuple of merged dimensions. However, the order of the original dimensions are not necessarily preserved.
+"""
+function unmergedims(merged_dims::Tuple{Vararg{Dimension}})
+    reduce(map(dims, merged_dims), init=()) do acc, x
+        x isa Tuple ? (acc..., x...) : (acc..., x)
+    end
+end
+
+"""
+    unmergedims(A::AbstractDimArray, original_dims) => AbstractDimArray
+    unmergedims(A::AbstractDimStack, original_dims) => AbstractDimStack
+
+Return a new array or stack whose dimensions are restored to their original prior to calling [`mergedims(A, dim_pairs)`](@ref).
+"""
+function unmergedims(A::AbstractDimArray, original_dims)
+    merged_dims = dims(A)
+    unmerged_dims = unmergedims(merged_dims)
+    reshaped = reshape(data(A), size(unmerged_dims))
+    permuted = permutedims(reshaped, dimnum(unmerged_dims, original_dims))
+    return DimArray(permuted, original_dims)
+end
+
+function _mergedims(all_dims, dim_pair::Pair, dim_pairs::Pair...)
+    old_dims, new_dim = dim_pair
+    dims_to_merge = dims(all_dims, _astuple(old_dims))
+    merged_dim = mergedims(dims_to_merge => new_dim)
+    all_dims_new = (otherdims(all_dims, dims_to_merge)..., merged_dim)
+    isempty(dim_pairs) && return all_dims_new
+    return _mergedims(all_dims_new, dim_pairs...)
+end
+
+function _unmergedims(all_dims, merged_dims)
+    _merged_dims = dims(all_dims, merged_dims)
+    unmerged_dims = map(all_dims) do d
+        hasdim(_merged_dims, d) || return _astuple(d)
+        return dims(lookup(d))
+    end
+    return _cat_tuples(unmerged_dims...)
+end
+
+_unmergedims(all_dims, dim_pairs::Pair...) = _cat_tuples(replace(all_dims, dim_pairs...))
+
+_cat_tuples(tuples...) = mapreduce(_astuple, (x, y) -> (x..., y...), tuples)
+
+_filter_dims(alldims, dims) = filter(dim -> hasdim(alldims, dim), dims)

src/stack/stack.jl

@@ -157,6 +157,17 @@ for func in (:index, :lookup, :metadata, :sampling, :span, :bounds, :locus, :ord
     @eval ($func)(s::AbstractDimStack, args...) = ($func)(dims(s), args...)
 end
 
+function mergedims(ds::AbstractDimStack, dim_pairs::Pair...)
+    isempty(dim_pairs) && return ds
+    vals = map(A -> mergedims(A, dim_pairs...), values(ds))
+    rebuild_from_arrays(ds, vals)
+end
+
+function unmergedims(s::AbstractDimStack, original_dims)
+    return map(A -> unmergedims(A, original_dims), s)
+end
+
+
 """
     DimStack <: AbstractDimStack