# Write structure to HDF5 file and read a compound type from HDF5 into Julia structure

**URL:** <https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358>\
**Category:** General Usage\
**Tags:** hdf5\
**Created:** [February 1, 2019, 4:04pm UTC](https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358 "2019-02-01T16:04:27Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sairus7](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/sairus7/32/10816_2.png) [@sairus7](https://discourse.julialang.org/u/sairus7)\
**Post date:** [February 1, 2019, 4:04pm UTC](https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358/1 "2019-02-01T16:04:27Z")

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How to write a structure in HDF5 file?

```julia
using HDF5
mutable struct Foo
    a::Int
    b::Float64
end
vect = [1,2,3,4,5]
foo = Foo(1, 2.0)
foovect = [P(i, i/2) for i=1:5]
path = "/testfile.h5"
h5write(path, "/vect", vect)
h5write(path, "/foo", foo) 
# > MethodError: no method matching write(::HDF5File, ::String, ::Foo)
h5write(path, "/foovec", foovect)
# > MethodError: no method matching write(::HDF5File, ::String, ::Array{P,1})

```

And how to read a compound type?  
If I write some compound type into a hdf5 with c++ (`Hello World!` into a byte fields named as `field0` … `field11`), then try to read it in Julia, it reads an array of `HDF5Compound` type:

```julia
HDF5.HDF5Compound{12}
data -> (0x48, 0x65, 0x6c, 0x6c, 0x6f, 0x20, 0x57, 0x6f, 0x72, 0x6c, 0x64, 0x21), 
membername -> ("0\xfd\xf6\x11field0", "0\xfd\xf6\x11field1", "0\xfd\xf6\x11field2", "0\xfd\xf6\x11field3", "0\xfd\xf6\x11field4", "0\xfd\xf6\x11field5", "0\xfd\xf6\x11field6", "0\xfd\xf6\x11field7", "0\xfd\xf6\x11field8", "0\xfd\xf6\x11field9", "0\xfd\xf6\x11field10", "0\xfd\xf6\x11field11"), 
membertype -> (UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8, UInt8))

```

Can it be converted into a structure or named tuple or something?

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<div class="post-metadata">

**Author:** ![tobias.knopp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tobias.knopp/32/7551_2.png) [@tobias.knopp](https://discourse.julialang.org/u/tobias.knopp)\
**Post date:** [February 2, 2019, 7:56am UTC](https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358/2 "2019-02-02T07:56:37Z")

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you have to do this manually. I have an example for reading here:

[https://github.com/MagneticResonanceImaging/MRIReco.jl/blob/master/src/IO/ISMRMRD.jl#L59](https://github.com/MagneticResonanceImaging/MRIReco.jl/blob/master/src/IO/ISMRMRD.jl#L59)

And here is an example for writing a compound data type:

> <https://github.com/MagneticParticleImaging/MPIFiles.jl/blob/master/src/MPIFiles.jl#L384>

Of course it would be great to have something which does this automatically.

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<div class="post-metadata">

**Author:** ![tamasgal](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamasgal/32/27946_2.png) [@tamasgal](https://discourse.julialang.org/u/tamasgal)\
**Post date:** [February 2, 2019, 10:09am UTC](https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358/3 "2019-02-02T10:09:26Z")

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I have these two functions to read compound structures, given that you have a `struct` with the corresponding layout:

```julia
function read_compound(dset::HDF5.HDF5Dataset, T::DataType)
    filetype = HDF5.datatype(dset)
    memtype_id = HDF5.h5t_get_native_type(filetype.id)
    @assert sizeof(T) == HDF5.h5t_get_size(memtype_id) "type size mismatch"
    out = Vector{T}(undef, length(dset))
    HDF5.h5d_read(dset.id, memtype_id, HDF5.H5S_ALL, HDF5.H5S_ALL, HDF5.H5P_DEFAULT, out)
    HDF5.h5t_close(memtype_id)
    out
end

function read_compound(filename::AbstractString,
                       h5loc::AbstractString,
                       T::DataType)
    fobj = HDF5.h5open(filename)
    data = read_compound(fobj[h5loc], T)
    close(fobj)
    data
end

```

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**Author:** ![jacob-roth](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jacob-roth/32/1862_2.png) [@jacob-roth](https://discourse.julialang.org/u/jacob-roth)\
**Post date:** [June 18, 2019, 1:58am UTC](https://discourse.julialang.org/t/write-structure-to-hdf5-file-and-read-a-compound-type-from-hdf5-into-julia-structure/20358/4 "2019-06-18T01:58:17Z")

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How can I save an array of arrays in HDF5? In particular, I’m trying to save an array of `Set`s, but HDF5 can’t save a `Set`, so I tried converting to an array, but I still cant save an array of arrays. I’m trying `HDF5` over `JLD2` because of what I think are similar mapping / serialization issues referenced [here](https://github.com/JuliaIO/JLD2.jl/issues/55)…