Integration of CommonDataModel sources #416

tcarion · 2023-04-14T12:26:38Z

This should allow reading any dataset that implements CommonDataModel.jl. It would solve #282

rafaqz · 2023-04-14T12:41:02Z

Awesome!

I would really like to get it working (properly) with lazy=true, which will need changes to CommonDataModel.jl

tcarion · 2023-04-14T14:37:51Z

For GRIBDataset, lazy = true on RasterStack works if you consider the PR JuliaGeo/CommonDataModel.jl#9. However, it fails with lazy = false! It actually fails when using the read method on RasterStack's (see below). I'm trying to understand why.

lazystack= RasterStack(era5; lazy=true)
read(lazystack)
ERROR: MethodError: no method matching _maybestack(::RasterStack{Rasters.OpenStack{Rasters.GRIBfile, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing}, ::Tuple{Raster{Float64, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, Array{Float64, 5}, Symbol, Metadata{CDMfile, Dict{String, Any}}, Missing}, Raster{Float64, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, Array{Float64, 5}, Symbol, Metadata{CDMfile, Dict{String, Any}}, Missing}})
Closest candidates are:
  _maybestack(::AbstractDimStack{<:NamedTuple{K}}, ::Tuple{AbstractDimArray, Vararg{AbstractDimArray}}) where K at ~/.julia/packages/DimensionalData/7iYMt/src/stack/methods.jl:72
  _maybestack(::AbstractDimStack{<:NamedTuple{K}}, ::Tuple) where K at ~/.julia/packages/DimensionalData/7iYMt/src/stack/methods.jl:69
Stacktrace:
 [1] map(f::Function, s::RasterStack{Rasters.OpenStack{Rasters.GRIBfile, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing})
   @ DimensionalData ~/.julia/packages/DimensionalData/7iYMt/src/stack/methods.jl:51
 [2] (::Rasters.var"#97#99"{UnionAll})(o::RasterStack{Rasters.OpenStack{Rasters.GRIBfile, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing})
   @ Rasters ~/.julia/dev/Rasters/src/stack.jl:326
 [3] open(f::Rasters.var"#97#99"{UnionAll}, st::RasterStack{Rasters.FileStack{Rasters.GRIBfile, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing}; kw::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Rasters ~/.julia/dev/Rasters/src/stack.jl:333
 [4] open(f::Function, st::RasterStack{Rasters.FileStack{Rasters.GRIBfile, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing})
   @ Rasters ~/.julia/dev/Rasters/src/stack.jl:332
 [5] modify(f::Type, s::RasterStack{Rasters.FileStack{Rasters.GRIBfile, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing})
   @ Rasters ~/.julia/dev/Rasters/src/stack.jl:325
 [6] read(x::RasterStack{Rasters.FileStack{Rasters.GRIBfile, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMfile, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMfile, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMfile, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMfile, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMfile, Dict{String, Any}}, Metadata{CDMfile, Dict{String, Any}}}}, Missing})
   @ Rasters ~/.julia/dev/Rasters/src/read.jl:9

rafaqz · 2023-04-14T14:59:44Z

Ahh this is just a DimensionalData.jl bug im in the process of fixing.

Downgrade DD to 0.24.4 or thereabouts for now.

Also, good to set DiskArrays.allow_scalar(false) to make sure it does really work. Then test some broadcasts with read or indexing afterwards.

(All the tests should actually have allow_scalar set to false but they were written befire I added it to DiskArrays)

Conflicts: src/Rasters.jl src/convenience.jl src/sources/commondatamodel.jl

tcarion · 2023-04-17T14:57:41Z

I updated according to #421, thanks for noticing me!
Using [email protected], it goes further but still fails:

julia> read(lazystack)
ERROR: No dims found
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] dims(#unused#::Nothing)
    @ DimensionalData.Dimensions ~/.julia/packages/DimensionalData/bJAtd/src/Dimensions/dimension.jl:169
  [3] map
    @ ./tuple.jl:221 [inlined]
  [4] combinedims(xs::Nothing; kw::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ DimensionalData.Dimensions ~/.julia/packages/DimensionalData/bJAtd/src/Dimensions/primitives.jl:528
  [5] combinedims
    @ ~/.julia/packages/DimensionalData/bJAtd/src/Dimensions/primitives.jl:528 [inlined]
  [6] #combinedims#45
    @ ~/.julia/packages/DimensionalData/bJAtd/src/Dimensions/primitives.jl:528 [inlined]
  [7] combinedims
    @ ~/.julia/packages/DimensionalData/bJAtd/src/Dimensions/primitives.jl:528 [inlined]
  [8] (::Rasters.var"#71#72"{NamedTuple{(:z, :t), Tuple{Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}, Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}}}})()
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:88
  [9] #invokelatest#2
    @ ./essentials.jl:716 [inlined]
 [10] invokelatest
    @ ./essentials.jl:714 [inlined]
 [11] rebuild_from_arrays(s::RasterStack{Rasters.OpenStack{Rasters.GRIBsource, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing}, das::NamedTuple{(:z, :t), Tuple{Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}, Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}}}; data::NamedTuple{(:z, :t), Tuple{Array{Union{Missing, Float64}, 5}, Array{Union{Missing, Float64}, 5}}}, refdims::Tuple{}, metadata::Metadata{CDMsource, Dict{String, Any}}, dims::Nothing, layerdims::NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, layermetadata::NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, missingval::NamedTuple{(:z, :t), Tuple{Missing, Missing}})
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:87
 [12] rebuild_from_arrays
    @ ~/.julia/dev/Rasters/src/stack.jl:85 [inlined]
 [13] _maybestack(s::RasterStack{Rasters.OpenStack{Rasters.GRIBsource, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing}, das::NamedTuple{(:z, :t), Tuple{Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}, Raster{Union{Missing, Float64}, 5, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, Array{Union{Missing, Float64}, 5}, Symbol, Metadata{CDMsource, Dict{String, Any}}, Missing}}})
    @ DimensionalData ~/.julia/packages/DimensionalData/bJAtd/src/stack/methods.jl:99
 [14] map(f::Function, s::RasterStack{Rasters.OpenStack{Rasters.GRIBsource, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing})
    @ DimensionalData ~/.julia/packages/DimensionalData/bJAtd/src/stack/methods.jl:50
 [15] (::Rasters.var"#98#100"{UnionAll})(o::RasterStack{Rasters.OpenStack{Rasters.GRIBsource, (:z, :t), GRIBDataset{Float64, 5}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing})
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:316
 [16] open(f::Rasters.var"#98#100"{UnionAll}, st::RasterStack{Rasters.FileStack{Rasters.GRIBsource, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing}; kw::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:323
 [17] open(f::Function, st::RasterStack{Rasters.FileStack{Rasters.GRIBsource, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing})
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:322
 [18] modify(f::Type, s::RasterStack{Rasters.FileStack{Rasters.GRIBsource, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing})
    @ Rasters ~/.julia/dev/Rasters/src/stack.jl:315
 [19] read(x::RasterStack{Rasters.FileStack{Rasters.GRIBsource, (:z, :t), String, Tuple{Union, Union}, Tuple{NTuple{5, Int64}, NTuple{5, Int64}}, Tuple{DiskArrays.GridChunks{5}, DiskArrays.GridChunks{5}}, Tuple{DiskArrays.Unchunked, DiskArrays.Unchunked}}, Tuple{X{Mapped{Float64, Vector{Float64}, ForwardOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, X{Colon}}}, Y{Mapped{Float64, Vector{Float64}, ReverseOrdered, Regular{Float64}, Points, Metadata{CDMsource, Dict{String, Any}}, EPSG, EPSG, Y{Colon}}}, Z{Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Dim{:number, Sampled{Int64, Vector{Int64}, ForwardOrdered, Regular{Int64}, Points, Metadata{CDMsource, Dict{String, Any}}}}, Ti{Sampled{DateTime, Vector{DateTime}, ForwardOrdered, Irregular{Tuple{Nothing, Nothing}}, Points, Metadata{CDMsource, Dict{String, Any}}}}}, Tuple{}, NamedTuple{(:z, :t), Tuple{Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}, Tuple{X{Colon}, Y{Colon}, Z{Colon}, Dim{:number, Colon}, Ti{Colon}}}}, Metadata{CDMsource, Dict{String, Any}}, NamedTuple{(:z, :t), Tuple{Metadata{CDMsource, Dict{String, Any}}, Metadata{CDMsource, Dict{String, Any}}}}, Missing})
    @ Rasters ~/.julia/dev/Rasters/src/read.jl:9

rafaqz · 2023-04-17T21:07:38Z

This will give a different error on the latests DD.

But Im guessing something is missing a dims method? You are calling combinedims on nothing

tcarion · 2023-04-18T11:34:04Z

Thanks, it indeed works with the latest commit of DD (after a minor fix)!
So GRIBDataset works, next is to fix it for NCDataset, which I'll work on once Alexander-Barth/NCDatasets.jl#205 is done

src/Rasters.jl src/sources/commondatamodel.jl test/runtests.jl

codecov-commenter · 2023-07-05T09:54:26Z

Codecov Report

Attention: 29 lines in your changes are missing coverage. Please review.

Comparison is base (c63af55) 80.99% compared to head (a453b21) 80.93%.

❗ Current head a453b21 differs from pull request most recent head 4f38942. Consider uploading reports for the commit 4f38942 to get more accurate results

Files	Patch %	Lines
src/sources/commondatamodel.jl	87.39%	29 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #416      +/-   ##
==========================================
- Coverage   80.99%   80.93%   -0.06%     
==========================================
  Files          58       61       +3     
  Lines        4204     4218      +14     
==========================================
+ Hits         3405     3414       +9     
- Misses        799      804       +5

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tcarion · 2023-07-07T08:07:00Z

@rafaqz, I tried to implement your idea here. Can you confirm that's what you had in mind?
The tests are passing locally with the DiskArray branch of NCDatasets.

If it's ok for you, I'll look into the grow! method.

rafaqz · 2023-07-07T08:48:59Z

Looks good! but we probably need to define the chunking?

rafaqz · 2023-09-29T09:34:03Z

Hey @tcarion where are we at with merging this now we have DiskArrays methods for NCDatasets.Variable ?

I'm sorry this has all taken so long, I can help get this over the line if there are any remaining issues.

Conflicts: Project.toml ext/RastersNCDatasetsExt/ncdatasets_source.jl

tcarion · 2023-10-09T12:29:16Z

Since NCDatasets has been yanked, the tests are failing here, but it works locally with v0.13. If I get it well, the issue Alexander-Barth/NCDatasets.jl#230 is solved thanks to meggart/DiskArrays.jl#124, is that right @Alexander-Barth ? If so, the tests should pass when we're back at v0.13 (I hope)

rafaqz · 2023-10-09T13:55:27Z

It could be unyanked now that DiskArrays is fixed, @Alexander-Barth

Alexander-Barth · 2023-10-10T10:15:22Z

I just released NCDatasets 0.13.1 with DiskArray support.
Note at some point I would like to have a ZarrDatasets package implementing the CommonDataModel.jl interface for zarr files (based on Zarr.jl).
Maybe this will also be helpful for Rasters.jl package or does it already have zarr support by other means?

rafaqz · 2023-10-10T10:53:43Z

Yes that would be good to have!

Conflicts: Project.toml

rafaqz · 2024-01-01T09:57:44Z

@tcarion would it help if I finished this off? there have been a bunch of changes since this branched

Conflicts: Project.toml test/sources/ncdatasets.jl

tcarion · 2024-01-18T09:28:58Z

@rafaqz Do you think this can be merged now ? The tests won't pass on Windows, which is normal since GRIB.jl doesn't support Windows for now

rafaqz · 2024-01-18T12:56:04Z

Everything has to pass to be merged, but that may just mean skipping the grib tests on windows with a condition in the runtests.jl file. But yes otherwise this looks really good.

There are also failing documenter tests but that looks like something different.

rafaqz · 2024-01-18T20:18:35Z

Ok I'm going to merge and fix the makie documentation errors later.

Thanks so much for pushing this through!!

rafaqz · 2024-01-19T01:25:11Z

Note that DiskArrays doesn't actually work with this PR. chunks have to be forwarded down to the wrapped array that knows about them, and CommonDataModel.jl doesn't.

@Alexander-Barth CommonDataModel.jl variables not being disk arrays is really killing us here, the complexity of making it actually work with hacks is a huge overhead I would rather not deal with.

tcarion added 2 commits April 14, 2023 13:57

adapt ncdatasets source for commondatamodel

8f295ce

rename sources/ncdatasets.jl

ff6be22

tcarion mentioned this pull request Apr 14, 2023

DiskArrays for CFVariable JuliaGeo/CommonDataModel.jl#9

Draft

Merge branch 'main' into commondatamodel

08ab1fe

Conflicts: src/Rasters.jl src/convenience.jl src/sources/commondatamodel.jl

fix for lazy = false in stack

8b244f1

tcarion added 6 commits April 18, 2023 15:52

cf attributes

a231f2c

Conflicts:

e7bc1f9

src/Rasters.jl src/sources/commondatamodel.jl test/runtests.jl

reorganize project

45d3a54

Merge branch 'main' into commondatamodel

339033a

Merge branch 'rafaqz:main' into commondatamodel

58be792

move writing code to ncdatasets_source

715428c

tcarion mentioned this pull request Jul 4, 2023

DiskArrays for Variable's Alexander-Barth/NCDatasets.jl#205

Merged

tcarion added 5 commits July 4, 2023 15:22

fix error if dim not a coordinate

d069f7f

small fixes

9622536

issue with building dims for variables

1064bbd

fix grid mapping

3b1312a

comments in test

68e029b

diskarray wrapper for CFVariable

073a77d

rafaqz mentioned this pull request Jul 30, 2023

Will there ever be a convergence of NetCDF.jl and NCDatasets? JuliaGeo/NetCDF.jl#180

Open

Merge branch 'main' into commondatamodel

9fd5120

Conflicts: Project.toml ext/RastersNCDatasetsExt/ncdatasets_source.jl

update compat for NCDatasets

39d02ba

tcarion marked this pull request as ready for review October 18, 2023 08:03

tcarion added 2 commits October 18, 2023 10:21

update readme

60efd75

Merge branch 'main' into commondatamodel

f6a4e49

Conflicts: Project.toml

tcarion added 2 commits January 8, 2024 11:04

Merge branch 'main' into commondatamodel

92c1370

Conflicts: Project.toml test/sources/ncdatasets.jl

update GRIBDatasets compat

a453b21

rafaqz mentioned this pull request Jan 17, 2024

Write seems to consume a lot of memory #317

Closed

skip GRIBDatasets test on windows

4f38942

rafaqz merged commit a913761 into rafaqz:main Jan 18, 2024
5 of 7 checks passed

tcarion deleted the commondatamodel branch January 19, 2024 09:58

felixcremer mentioned this pull request May 13, 2024

Opening a multi variable NetCDF does not info anymore #669

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Integration of CommonDataModel sources #416

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