JuliaDataCubes / JuliaDataCubes/YAXArrayBase.jl

Can't save a YAXArray with Variable axes as netcdf

Open
#3 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Julia
Stars
3
Forks
9
PR merge metrics
No merged PRs in 30d

Description

When I try to save the following YAXArray

julia> imfextinds
YAXArray with the following dimensions
FrequencyStats      Axis with 6 elements: FirstLocalMax FirstLocalMin FirstZeroCrossing SecondLocMax SecondLocMin SecondZeroCross 
Y                   Axis with 5820 Elements from 561609.15 to 736179.15
X                   Axis with 7500 Elements from 9.48724066e6 to 9.26227066e6
Total size: 999.07 MB

this fails with the following error:

julia> savecube(imfextinds,"data/cubes/s1cube_jurua_vh_smallchunks_imfs_4_local_extinds_4_newesdl.nc", backend=:netcdf)
┌ Warning: There are still cache misses
└ @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:697
ERROR: ArgumentError: array must be non-empty
Stacktrace:
  [1] popfirst!
    @ ./array.jl:1288 [inlined]
  [2] jl2nc(t::DataType)
    @ NetCDF ~/.julia/packages/NetCDF/0sRUL/src/NetCDF.jl:90
  [3] getNCType(t::DataType)
    @ NetCDF ~/.julia/packages/NetCDF/0sRUL/src/NetCDF.jl:100
  [4] NcVar(name::String, dimin::Vector{NcDim}; atts::Dict{String, Any}, t::DataType, compress::Int64, chunksize::Tuple{Int64})
    @ NetCDF ~/.julia/packages/NetCDF/0sRUL/src/NetCDF.jl:255
  [5] nccreate(::String, ::String, ::String, ::Vararg{Any, N} where N; atts::Dict{String, Any}, gatts::Dict{Any, Any}, compress::Int64, t::DataType, mode::UInt16, chunksize::Tuple{Int64})
    @ NetCDF ~/.julia/packages/NetCDF/0sRUL/src/NetCDF.jl:1208
  [6] #add_var#75
    @ ~/.julia/packages/YAXArrayBase/OgYsV/src/datasets/netcdf.jl:50 [inlined]
  [7] add_var
    @ ~/.julia/packages/YAXArrayBase/OgYsV/src/datasets/netcdf.jl:49 [inlined]
  [8] #add_var#2
    @ ~/.julia/packages/YAXArrayBase/OgYsV/src/datasets/datasetinterface.jl:46 [inlined]
  [9] add_var
    @ ~/.julia/packages/YAXArrayBase/OgYsV/src/datasets/datasetinterface.jl:46 [inlined]
 [10] arrayfromaxis(p::YAXArrayBase.NetCDFDataset, ax::CategoricalAxis{Zarr.MaxLengthStrings.MaxLengthString{17, UInt8}, :FrequencyStats, Vector{Zarr.MaxLengthStrings.MaxLengthString{17, UInt8}}}, offs::Int64)
    @ YAXArrays.Datasets ~/.julia/dev/YAXArrays/src/DatasetAPI/Datasets.jl:319
 [11] (::YAXArrays.Datasets.var"#60#69"{YAXArrayBase.NetCDFDataset})(ax::CategoricalAxis{Zarr.MaxLengthStrings.MaxLengthString{17, UInt8}, :FrequencyStats, Vector{Zarr.MaxLengthStrings.MaxLengthString{17, UInt8}}}, co::Int64)
    @ YAXArrays.Datasets ~/.julia/dev/YAXArrays/src/DatasetAPI/Datasets.jl:253
 [12] foreach(::Function, ::Vector{CubeAxis}, ::Tuple{Int64, Int64, Int64})
    @ Base ./abstractarray.jl:2129
 [13] createdataset(DS::Type, axlist::Vector{CubeAxis}; path::String, persist::Nothing, T::Type, chunksize::Tuple{Int64, Int64, Int64}, chunkoffset::Tuple{Int64, Int64, Int64}, overwrite::Bool, properties::Dict{String, Any}, datasetaxis::String, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ YAXArrays.Datasets ~/.julia/dev/YAXArrays/src/DatasetAPI/Datasets.jl:252
 [14] generateOutCube(::Type{YAXArrayBase.NetCDFDataset}, eltype::Type, oc::YAXArrays.DAT.OutputCube, loopcachesize::Vector{Int64}, co::Tuple{Int64, Int64, Int64}; kwargs::Base.Iterators.Pairs{Symbol, String, Tuple{Symbol}, NamedTuple{(:path,), Tuple{String}}})
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:515
 [15] generateOutCube(oc::YAXArrays.DAT.OutputCube, ispar::Base.RefValue{Bool}, max_cache::Float64, loopcachesize::Vector{Int64}, co::Tuple{Int64, Int64, Int64})
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:539
 [16] (::YAXArrays.DAT.var"#106#107"{YAXArrays.DAT.DATConfig{1, 1}, Tuple{Int64}})(c::YAXArrays.DAT.OutputCube)
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:534
 [17] foreach(f::YAXArrays.DAT.var"#106#107"{YAXArrays.DAT.DATConfig{1, 1}, Tuple{Int64}}, itr::Tuple{YAXArrays.DAT.OutputCube})
    @ Base ./abstractarray.jl:2128
 [18] generateOutCubes(dc::YAXArrays.DAT.DATConfig{1, 1})
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:532
 [19] mapCube(::YAXArrays.DAT.var"#cop#260", ::Tuple{YAXArray{Union{Missing, Float32}, 3, Zarr.ZArray{Union{Missing, Float32}, 3, Zarr.BloscCompressor, Zarr.DirectoryStore}, Vector{CubeAxis}}}; max_cache::Float64, indims::InDims, outdims::OutDims, inplace::Bool, ispar::Bool, debug::Bool, include_loopvars::Bool, showprog::Bool, nthreads::Vector{Int64}, loopchunksize::Dict{Any, Any}, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:276
 [20] #mapCube#34
    @ ~/.julia/dev/YAXArrays/src/DAT/DAT.jl:178 [inlined]
 [21] savecube(c::YAXArray{Union{Missing, Float32}, 3, Zarr.ZArray{Union{Missing, Float32}, 3, Zarr.BloscCompressor, Zarr.DirectoryStore}, Vector{CubeAxis}}, name::String; chunksize::Dict{Any, Any}, max_cache::Float64, backend::Symbol, backendargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ YAXArrays.DAT ~/.julia/dev/YAXArrays/src/DAT/CubeIO.jl:38
 [22] top-level scope
    @ REPL[16]:1

but when I use subsetcube to separate one of the variables I can save it.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing savecube with the CategoricalAxis shown in the issue and follow the stack trace through YAXArrays/src/DatasetAPI/Datasets.jl and YAXArrayBase's datasets/netcdf.jl. Inspect the NetCDF.jl type handling at the reported jl2nc call. Done means a YAXArray with variable axes can be saved as NetCDF without requiring subsetcube.

Written by the indexing model from the issue text.

Assessment

Tech stack
julia
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.