I feel like I am over complicating this - HDF5 saving array

New to Julia
1

Hello guys

I want to save an array of the following type;

Array{Array{Float32,2},1}

I have called it “B” and I want to save it in a hdf5 file. It gives me an error, with no method matching and I don’t know how to get past it. It works if I try to save only a part of B, ie. B[1], but does not work if I try to save the whole array directly. I am pretty sure I am misunderstanding something very simple, so I hope someone could push me in the right direction?

Kind regards

using HDF5

 B = Vector{Array{Float32,2}}(undef,3)
 B[1] = rand(3,3);
 B[2] = rand(3,3);
 B[3] = rand(3,3);

h5open("B.hdf5", "w") do file
    write(file, "B",B)  # alternatively, say "@write file A"
    close(file)
end
2

Is HDF5 a requirement? If not then you can use JLD.jl or JLD2.jl. I believe they both used different modified HDF5 formats.

3

I just thought that the hdf5.jl package was the best developed, so that is why I chose it. It seems like they use the same syntax, so I would still not know how to save my B array - could you help me out with that?

Kind regards

4

HDF5 will save arrays of numeric types (eg Int64, Float64, etc) but it won’t save more complicated types by default. You can either save the vector elements yourself like

 B = Vector{Array{Float32,2}}(undef,3)
 B[1] = rand(3,3);
 B[2] = rand(3,3);
 B[3] = rand(3,3);

h5open("B.hdf5", "w") do file
    file["B1"] = B[1]
    file["B2"] = B[2]
    file["B3"] = B[3]
end

Or use a 3d array instead of a vector of 2d arrays like

C = zeros(3,3,3)
C[1,:,:] = rand(3,3);
C[2,:,:] = rand(3,3);
C[3,:,:] = rand(3,3);
h5open("C.hdf5", "w") do file
    file["C"]=C
end

I would recommend HDF5 over JLD if you want your data to be accesible to non-julia users, and if you don’t have super complicated data structures.

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