Wrapping an array with AxisArrays breaks PNGFiles

[tlnagy]

I ran into this when working with OMETIFF.jl returned AxisArray objects in IJulia, which uses PNGFiles for display:

julia> using FixedPointNumbers, Colors, PNGFiles, AxisArrays

julia> img = rand(Gray{N0f16}, 100, 100);

julia> PNGFiles.save("img.png", img); # works as expected

julia> PNGFiles.save("img2.png", AxisArray(img)); # wrapped with AxisArrays
ERROR: conversion to pointer not defined for AxisArray{Gray{N0f16}, 1, SubArray{Gray{N0f16}, 1, Matrix{Gray{N0f16}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}, Tuple{Axis{:col, Base.OneTo{Int64}}}}
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] unsafe_convert(#unused#::Type{Ptr{Gray{N0f16}}}, a::AxisArray{Gray{N0f16}, 1, SubArray{Gray{N0f16}, 1, Matrix{Gray{N0f16}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}, Tuple{Axis{:col, Base.OneTo{Int64}}}})
    @ Base ./pointer.jl:67
  [3] pointer(x::AxisArray{Gray{N0f16}, 1, SubArray{Gray{N0f16}, 1, Matrix{Gray{N0f16}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}, Tuple{Axis{:col, Base.OneTo{Int64}}}})
    @ Base ./abstractarray.jl:1116
  [4] iterate
    @ ./generator.jl:47 [inlined]
  [5] collect(itr::Base.Generator{Base.Generator{Base.OneTo{Int64}, Base.var"#193#194"{AxisArray{Gray{N0f16}, 2, Matrix{Gray{N0f16}}, Tuple{Axis{:col, Base.OneTo{Int64}}, Axis{:row, Base.OneTo{Int64}}}}}}, typeof(pointer)})
    @ Base ./array.jl:681
  [6] map
    @ ./abstractarray.jl:2323 [inlined]
  [7] _write_image(buf::AxisArray{Gray{N0f16}, 2, Matrix{Gray{N0f16}}, Tuple{Axis{:col, Base.OneTo{Int64}}, Axis{:row, Base.OneTo{Int64}}}}, png_ptr::Ptr{Nothing}, info_ptr::Ptr{Nothing})
    @ PNGFiles ~/.julia/packages/PNGFiles/dIbpb/src/io.jl:430
  [8] _save(png_ptr::Ptr{Nothing}, info_ptr::Ptr{Nothing}, image::AxisArray{Gray{N0f16}, 2, Matrix{Gray{N0f16}}, Tuple{Axis{:row, Base.OneTo{Int64}}, Axis{:col, Base.OneTo{Int64}}}}; compression_level::Int64, compression_strategy::Int64, filters::Int64, palette::Nothing)
    @ PNGFiles ~/.julia/packages/PNGFiles/dIbpb/src/io.jl:418
  [9] save(fpath::String, image::AxisArray{Gray{N0f16}, 2, Matrix{Gray{N0f16}}, Tuple{Axis{:row, Base.OneTo{Int64}}, Axis{:col, Base.OneTo{Int64}}}}; compression_level::Int64, compression_strategy::Int64, filters::Int64, palette::Nothing)
    @ PNGFiles ~/.julia/packages/PNGFiles/dIbpb/src/io.jl:298
 [10] save(fpath::String, image::AxisArray{Gray{N0f16}, 2, Matrix{Gray{N0f16}}, Tuple{Axis{:row, Base.OneTo{Int64}}, Axis{:col, Base.OneTo{Int64}}}})
    @ PNGFiles ~/.julia/packages/PNGFiles/dIbpb/src/io.jl:284
 [11] top-level scope
    @ REPL[5]:1

This breaks IJulia's display of AxisArrays:

Thoughts @IanButterworth @johnnychen94 ?

[johnnychen94]

Yep, this is a known ImageShow issue JuliaImages/ImageShow.jl#40 and also JuliaImages/ImageShow.jl#39

We can fix it in both ImageShow in https://github.com/JuliaImages/ImageShow.jl/blob/953f8e61ef5ef5b62845258a1a29c19f5cb93fa9/src/showmime.jl#L23-L47, and in PNGFiles to eagerly collect all unrecognized array types into dense array.

[tlnagy]

Thanks for the extremely rapid fix @johnnychen94! If you're ever in San Francisco, I owe you a 🍺 :)