Add support for reading H5T_ARRAY

src/plain.jl

@@ -4,10 +4,10 @@
 
 module HDF5
 
-include("datafile.jl")
-
 ## Add methods to...
-import Base: close, convert, done, dump, endof, flush, getindex, has, isempty, isvalid, length, names, ndims, next, read, setindex!, show, size, start, write
+import Base: close, convert, done, dump, eltype, endof, flush, getindex, has, isempty, isvalid, length, names, ndims, next, read, setindex!, show, size, start, write
+
+include("datafile.jl")
 
 ## C types
 typealias C_time_t Int
@@ -388,6 +388,13 @@ end
 # An empty array type
 type EmptyArray{T}; end
 
+# Stub types to encode fixed-size arrays for H5T_ARRAY
+immutable DimSize{N}; end # Int-wrapper (can't use tuple of Int as param)
+immutable FixedArray{T,D<:(DimSize...)}; end
+dimsize{N}(::Type{DimSize{N}}) = N
+size{T,D}(::Type{FixedArray{T,D}}) = map(dimsize, D)::(Int...)
+eltype{T,D}(::Type{FixedArray{T,D}}) = T
+
 # VLEN objects
 type HDF5Vlen{T}
  data
@@ -965,9 +972,7 @@ function read{T<:HDF5BitsKind}(obj::DatasetOrAttribute, ::Type{T})
 end
 # Read array of BitsKind
 function read{T<:HDF5BitsKind}(obj::DatasetOrAttribute, ::Type{Array{T}})
- local data
  dims = size(obj)
- dspace = dataspace(obj)
  data = Array(T, dims...)
  readarray(obj, hdf5_type_id(T), data)
  data
@@ -976,6 +981,38 @@ end
 function read{T<:BitsKindOrByteString}(obj::DatasetOrAttribute, ::Type{EmptyArray{T}})
  Array(T, 0)
 end
+# Fixed-size arrays (H5T_ARRAY)
+function read{A<:FixedArray}(obj::DatasetOrAttribute, ::Type{A})
+ T = eltype(A)
+ sz = size(A)
+ data = Array(T, sz)
+ readarray(obj, hdf5_type_id(T), data)
+ data
+end
+function read{A<:FixedArray}(obj::DatasetOrAttribute, ::Type{Array{A}})
+ T = eltype(A)
+ if !(T<:HDF5BitsKind)
+ error("Sorry, not yet supported")
+ end
+ sz = size(A)
+ dims = size(obj)
+ data = Array(T, tuple(sz..., dims...))
+ nd = length(sz)
+ hsz = Hsize[convert(Hsize,sz[nd-i+1]) for i = 1:nd]
+ memtype_id = h5t_array_create(hdf5_type_id(T), convert(Cuint, length(sz)), hsz)
+ try
+ h5d_read(obj.id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data)
+ finally
+ h5t_close(memtype_id)
+ end
+ ret = Array(Array{T}, dims)
+ # Because of garbage-collection concerns, it's best to copy the data
+ L = prod(sz)
+ for i = 1:prod(dims)
+ ret[i] = reshape(data[(i-1)*L+1:i*L], sz)
+ end
+ ret
+end
 
 # Clean up string buffer according to padding mode
 function unpad(s::ByteString, pad::Cint)
@@ -1497,6 +1534,8 @@ function hdf5_to_julia_eltype(objtype)
  T = HDF5Vlen{hdf5_to_julia_eltype(HDF5Datatype(super_id))}
  elseif class_id == H5T_COMPOUND
  T = HDF5Compound
+ elseif class_id == H5T_ARRAY
+ T = hdf5array(objtype)
  else
  error("Class id ", class_id, " is not yet supported")
  end
@@ -1724,8 +1763,11 @@ for (jlname, h5name, outtype, argtypes, argsyms, ex_error) in
  (:h5s_get_simple_extent_dims, :H5Sget_simple_extent_dims, Cint, (Hid, Ptr{Hsize}, Ptr{Hsize}), (:space_id, :dims, :maxdims), :(error("Error getting the dimensions for a dataspace"))),
  (:h5s_get_simple_extent_ndims, :H5Sget_simple_extent_ndims, Cint, (Hid,), (:space_id,), :(error("Error getting the number of dimensions for a dataspace"))),
  (:h5s_get_simple_extent_type, :H5Sget_simple_extent_type, Cint, (Hid,), (:space_id,), :(error("Error getting the dataspace type"))),
+ (:h5t_array_create, :H5Tarray_create2, Hid, (Hid, Cuint, Ptr{Hsize}), (:basetype_id, :ndims, :sz), :(error("Error creating H5T_ARRAY of id ", basetype_id, " and size ", sz))),
  (:h5t_copy, :H5Tcopy, Hid, (Hid,), (:dtype_id,), :(error("Error copying datatype"))),
  (:h5t_create, :H5Tcreate, Hid, (Cint, Csize_t), (:class_id, :sz), :(error("Error creating datatype of id ", classid))),
+ (:h5t_get_array_dims, :H5Tget_array_dims2, Cint, (Hid, Ptr{Hsize}), (:dtype_id, :dims), :(error("Error getting dimensions of array"))),
+ (:h5t_get_array_ndims, :H5Tget_array_ndims, Cint, (Hid,), (:dtype_id,), :(error("Error getting ndims of array"))),
  (:h5t_get_class, :H5Tget_class, Cint, (Hid,), (:dtype_id,), :(error("Error getting class"))),
  (:h5t_get_cset, :H5Tget_cset, Cint, (Hid,), (:dtype_id,), :(error("Error getting character set encoding"))),
  (:h5t_get_member_class, :H5Tget_member_class, Cint, (Hid, Cuint), (:dtype_id, :index), :(error("Error getting class of compound datatype member #", index))),
@@ -1855,6 +1897,16 @@ function vlen_get_buf_size(dset::HDF5Dataset, dtype::HDF5Datatype, dspace::HDF5D
  sz[1]
 end
 
+function hdf5array(objtype)
+ nd = h5t_get_array_ndims(objtype.id)
+ dims = Array(Hsize, nd)
+ h5t_get_array_dims(objtype.id, dims)
+ eltyp = HDF5Datatype(h5t_get_super(objtype.id))
+ T = hdf5_to_julia_eltype(eltyp)
+ dimsizes = ntuple(nd, i->DimSize{int(dims[nd-i+1])}) # reverse order
+ FixedArray{T, dimsizes}
+end
+
 ### Property manipulation ###
 get_create_properties(dset::HDF5Dataset) = HDF5Properties(h5d_get_create_plist(dset.id))
 get_create_properties(g::HDF5Group) = HDF5Properties(h5g_get_create_plist(dset.id))

test/readremote.jl

@@ -17,6 +17,29 @@ opq = Array{Uint8}[[0x4f, 0x50, 0x41, 0x51, 0x55, 0x45, 0x30],
  [0x4f, 0x50, 0x41, 0x51, 0x55, 0x45, 0x31],
  [0x4f, 0x50, 0x41, 0x51, 0x55, 0x45, 0x32],
  [0x4f, 0x50, 0x41, 0x51, 0x55, 0x45, 0x33]]
+# For H5T_ARRAY
+AA = Array{Int,2}[
+[ 0 0 0;
+ 0 -1 -2;
+ 0 -2 -4;
+ 0 -3 -6;
+ 0 -4 -8],
+[ 0 1 2;
+ 1 1 1;
+ 2 1 0;
+ 3 1 -1;
+ 4 1 -2],
+[ 0 2 4;
+ 2 3 4;
+ 4 4 4;
+ 6 5 4;
+ 8 6 4],
+[ 0 3 6;
+ 3 5 7;
+ 6 7 8;
+ 9 9 9;
+ 12 11 10]]
+
 
 const savedir = joinpath(tempdir(), "h5")
 if !isdir(savedir)
@@ -132,3 +155,9 @@ d = read(fid, "DS1")
 @assert d.tag == "Character array"
 @assert d.data == opq
 close(fid)
+
+file = getfile("h5ex_t_array.h5")
+fid = h5open(file, "r")
+A = read(fid, "DS1")
+@assert A == AA
+close(fid)