Unpad fixed length strings in compound datatypes (#614)

* wrap H5Tset_strpad

* add test for unpadding strings inside compound datasets

* unpad fixed strings in compound datasets

src/HDF5.jl

@@ -483,10 +483,13 @@ size(x::T) where T <: FixedArray = size(T)
 eltype(::Type{FixedArray{T,D,L}}) where {T,D,L} = T
 eltype(x::T) where T <: FixedArray = eltype(T)
 
-struct FixedString{N}
+struct FixedString{N, PAD}
   data::NTuple{N, Cchar}
 end
-length(::Type{FixedString{N}}) where N = N
+length(::Type{FixedString{N, PAD}}) where {N, PAD} = N
+length(x::T) where T <: FixedString = length(T)
+pad(::Type{FixedString{N, PAD}}) where {N, PAD} = PAD
+pad(x::T) where T <: FixedString = pad(T)
 
 struct VariableArray{T}
   len::Csize_t
@@ -1471,7 +1474,7 @@ end
 normalize_types(x) = x
 normalize_types(x::NamedTuple{T}) where T = NamedTuple{T}(map(normalize_types, values(x)))
 normalize_types(x::Cstring) = unsafe_string(x)
-normalize_types(x::FixedString) = join(Char.(x.data))
+normalize_types(x::FixedString) = unpad(join(Char.(x.data)), pad(x))
 normalize_types(x::FixedArray) = reshape(collect(x.data), size(x)...)
 normalize_types(x::VariableArray) = copy(unsafe_wrap(Array, convert(Ptr{eltype(x)}, x.p), x.len, own=false))
 
@@ -1780,7 +1783,7 @@ _dropint() = ()
 
 # Write to a subset of a dataset using array slices: dataset[:,:,10] = array
 
-setindex!(dset::HDF5Dataset, x, I::Union{AbstractRange,Integer,Colon}...) = 
+setindex!(dset::HDF5Dataset, x, I::Union{AbstractRange,Integer,Colon}...) =
     _setindex!(dset, x, Base.to_indices(dset, I)...)
 function _setindex!(dset::HDF5Dataset, X::Array, I::Union{AbstractRange{Int},Int}...)
     T = hdf5_to_julia(dset)
@@ -2001,7 +2004,8 @@ function hdf5_to_julia_eltype(objtype)
               return Cstring
             else
               n = h5t_get_size(dtype.id)
-              return FixedString{Int(n)}
+              pad = h5t_get_strpad(dtype.id)
+              return FixedString{Int(n), pad}
             end
           elseif ci == H5T_VLEN
             superid = h5t_get_super(dtype.id)
@@ -2187,6 +2191,7 @@ for (jlname, h5name, outtype, argtypes, argsyms, msg) in
      (:h5t_close, :H5Tclose, Herr, (Hid,), (:dtype_id,), "Error closing datatype"),
      (:h5t_set_cset, :H5Tset_cset, Herr, (Hid, Cint), (:dtype_id, :cset), "Error setting character set in datatype"),
      (:h5t_set_size, :H5Tset_size, Herr, (Hid, Csize_t), (:dtype_id, :sz), "Error setting size of datatype"),
+     (:h5t_set_strpad, :H5Tset_strpad, Herr, (Hid, Cint), (:dtype_id, :sz), "Error setting size of datatype"),
      (:h5t_set_precision, :H5Tset_precision, Herr, (Hid, Csize_t), (:dtype_id, :sz), "Error setting precision of datatype"),
     )
 

test/compound.jl

@@ -14,15 +14,15 @@ end
 struct foo_hdf5
   a::Float64
   b::Cstring
-  c::NTuple{10, Cchar}
+  c::NTuple{20, Cchar}
   d::NTuple{9, ComplexF64}
   e::HDF5.Hvl_t
 end
 
 function unsafe_convert(::Type{foo_hdf5}, x::foo)
   foo_hdf5(x.a,
            Base.unsafe_convert(Cstring, x.b),
-           ntuple(i -> x.c[i], length(x.c)),
+           ntuple(i -> i <= length(x.c) ? x.c[i] : '\0', 20),
            ntuple(i -> x.d[i], length(x.d)),
            HDF5.Hvl_t(length(x.e), pointer(x.e))
           )
@@ -38,8 +38,9 @@ function datatype(::Type{foo_hdf5})
   HDF5.h5t_insert(dtype, "b", fieldoffset(foo_hdf5, 2), vlenstr_dtype)
 
   fixedstr_dtype = HDF5.h5t_copy(HDF5.H5T_C_S1)
-  HDF5.h5t_set_size(fixedstr_dtype, 10 * sizeof(Cchar))
+  HDF5.h5t_set_size(fixedstr_dtype, 20 * sizeof(Cchar))
   HDF5.h5t_set_cset(fixedstr_dtype, HDF5.H5T_CSET_UTF8)
+  HDF5.h5t_set_strpad(fixedstr_dtype, HDF5.H5T_STR_NULLPAD)
   HDF5.h5t_insert(dtype, "c", fieldoffset(foo_hdf5, 3), fixedstr_dtype)
 
   hsz = HDF5.Hsize[3,3]