Merge pull request #469 from JuliaIO/bja/array

support AbstractArrays

Author: bjarthur

src/HDF5.jl

@@ -1614,7 +1614,7 @@ for (privatesym, fsym, ptype) in
         end
         # Scalar types
         ($fsym)(parent::$ptype, name::String, data::Union{T, AbstractArray{T}}, plists...) where {T<:ScalarOrString} =
-            ($privatesym)(parent, name, data, plists...)
+            ($privatesym)(parent, name, isa(data,AbstractArray) ? collect(data) : data, plists...)
         # VLEN types
         ($fsym)(parent::$ptype, name::String, data::HDF5Vlen{T}, plists...) where {T<:Union{HDF5Scalar,CharType}} =
             ($privatesym)(parent, name, data, plists...)
@@ -1637,7 +1637,7 @@ for (privatesym, fsym, ptype, crsym) in
         end
         # Scalar types
         ($fsym)(parent::$ptype, name::String, data::Union{T, AbstractArray{T}}, plists...) where {T<:ScalarOrString} =
-            ($privatesym)(parent, name, data, plists...)
+            ($privatesym)(parent, name, isa(data,AbstractArray) ? collect(data) : data, plists...)
         # VLEN types
         ($fsym)(parent::$ptype, name::String, data::HDF5Vlen{T}, plists...) where {T<:Union{HDF5Scalar,CharType}} =
             ($privatesym)(parent, name, data, plists...)
@@ -1664,9 +1664,10 @@ function write(obj::DatasetOrAttribute, data::HDF5Vlen{T}) where {T<:Union{HDF5S
 end
 # For plain files and groups, let "write(obj, name, val)" mean "d_write"
 write(parent::Union{HDF5File, HDF5Group}, name::String, data::Union{T, AbstractArray{T}}, plists...) where {T<:ScalarOrString} =
-    d_write(parent, name, data, plists...)
+    d_write(parent, name, isa(data,AbstractArray) ? collect(data) : data, plists...)
 # For datasets, "write(dset, name, val)" means "a_write"
-write(parent::HDF5Dataset, name::String, data::Union{T, AbstractArray{T}}, plists...) where {T<:ScalarOrString} = a_write(parent, name, data, plists...)
+write(parent::HDF5Dataset, name::String, data::Union{T, AbstractArray{T}}, plists...) where {T<:ScalarOrString} =
+    a_write(parent, name, data, plists...)
 
 # Reading arrays using getindex: data = dset[:,:,10]
 function getindex(dset::HDF5Dataset, indices::Union{AbstractRange{Int},Int}...)
@@ -1928,12 +1929,16 @@ function h5a_write(attr_id::Hid, memtype_id::Hid, v::HDF5Vlen{T}) where {T<:Unio
     vp = vlenpack(v)
     h5a_write(attr_id, memtype_id, vp)
 end
-h5a_create(loc_id::Hid, name::String, type_id::Hid, space_id::Hid) = h5a_create(loc_id, name, type_id, space_id, _attr_properties(name), H5P_DEFAULT)
+h5a_create(loc_id::Hid, name::String, type_id::Hid, space_id::Hid) =
+    h5a_create(loc_id, name, type_id, space_id, _attr_properties(name), H5P_DEFAULT)
 h5a_open(obj_id::Hid, name::String) = h5a_open(obj_id, name, H5P_DEFAULT)
-h5d_create(loc_id::Hid, name::String, type_id::Hid, space_id::Hid) = h5d_create(loc_id, name, type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)
+h5d_create(loc_id::Hid, name::String, type_id::Hid, space_id::Hid) =
+    h5d_create(loc_id, name, type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)
 h5d_open(obj_id::Hid, name::String) = h5d_open(obj_id, name, H5P_DEFAULT)
-h5d_read(dataset_id::Hid, memtype_id::Hid, buf::AbstractArray) = h5d_read(dataset_id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)
-h5d_write(dataset_id::Hid, memtype_id::Hid, buf::AbstractArray) = h5d_write(dataset_id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)
+h5d_read(dataset_id::Hid, memtype_id::Hid, buf::AbstractArray) =
+    h5d_read(dataset_id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)
+h5d_write(dataset_id::Hid, memtype_id::Hid, buf::AbstractArray) =
+    h5d_write(dataset_id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)
 function h5d_write(dataset_id::Hid, memtype_id::Hid, str::String)
     ccall((:H5Dwrite, libhdf5), Herr, (Hid, Hid, Hid, Hid, Hid, Cstring), dataset_id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, str)
 end

test/plain.jl

@@ -378,7 +378,6 @@ end
 end == collect(1:16)
 
 # issue 463
-fn = tempname()
 f = h5open(fn, "w")
 s = SharedArray{UInt16}(3,4,5)
 s[1:end] = 1:length(s)
@@ -388,6 +387,48 @@ s2 = read(f,"/data")
 close(f)
 rm(fn)
 
+# issue 466
+f = h5open(fn, "w")
+data = rand(UInt16,2,3);
+pda_data = PermutedDimsArray(data,(2,1));
+write(f,"/data",pda_data)
+pda_data_readback = read(f,"/data")
+@test pda_data == pda_data_readback
+close(f)
+rm(fn)
+
+f = h5open(fn, "w")
+d=reshape(1:6,2,3)
+write(f,"/data",d)
+d2 = read(f,"/data")
+@test d == d2
+close(f)
+rm(fn)
+
+f = h5open(fn, "w")
+d=view(rand(2,3),:,1)
+write(f,"/data",d)
+d2 = read(f,"/data")
+@test d == d2
+close(f)
+rm(fn)
+
+f = h5open(fn, "w")
+d=Diagonal(1:10)
+write(f,"/data",d)
+d2 = read(f,"/data")
+@test d == d2
+close(f)
+rm(fn)
+
+f = h5open(fn, "w")
+r=1:10
+write(f,"/data",r)
+r2 = read(f,"/data")
+@test collect(r) == r2
+close(f)
+rm(fn)
+
 end # testset plain
 
 # test strings with null and undefined references