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Fix v0.16 HDF5 deprecations #172

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merged 2 commits into from
Feb 5, 2022
Merged

Fix v0.16 HDF5 deprecations #172

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6b8a460
Fix v0.16 HDF5 deprecations
musm Feb 5, 2022
55f33c2
fixup
musm Feb 5, 2022
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
[compat]
BufferedStreams = "0.4.1, 1"
CodecZlib = "0.5, 0.6, 0.7"
HDF5 = "0.14, 0.15, 0.16"
HDF5 = "0.16"
julia = "1.3"

[extras]
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36 changes: 19 additions & 17 deletions src/MAT_HDF5.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -88,18 +88,20 @@ function matopen(filename::AbstractString, rd::Bool, wr::Bool, cr::Bool, tr::Boo
if !cr && !isfile(filename)
error("File ", filename, " cannot be found")
end
pa = create_property(HDF5.H5P_FILE_ACCESS; fclose_degree = HDF5.H5F_CLOSE_STRONG)
fapl = HDF5.FileAccessProperties()
fapl.fclose_degree = :strong
if cr && (tr || !isfile(filename))
# We're truncating, so we don't have to check the format of an existing file
# Set the user block to 512 bytes, to save room for the header
p = create_property(HDF5.H5P_FILE_CREATE; userblock = 512)
f = HDF5.h5f_create(filename, HDF5.H5F_ACC_TRUNC, p.id, pa.id)
fcpl = HDF5.FileCreateProperties()
fcpl.userblock = 512
f = HDF5.API.h5f_create(filename, HDF5.API.H5F_ACC_TRUNC, fcpl, fapl)
writeheader = true
else
f = HDF5.h5f_open(filename, wr ? HDF5.H5F_ACC_RDWR : HDF5.H5F_ACC_RDONLY, pa.id)
f = HDF5.API.h5f_open(filename, wr ? HDF5.API.H5F_ACC_RDWR : HDF5.API.H5F_ACC_RDONLY, fapl)
writeheader = false
end
close(pa)
close(fapl)
fid = MatlabHDF5File(HDF5.File(f, filename), true, writeheader, 0, compress)
pathrefs = "/#refs#"
if haskey(fid.plain, pathrefs)
Expand Down Expand Up @@ -175,8 +177,8 @@ function m_read(dset::HDF5.Dataset)
# Check for a COMPOUND data set, and if so handle complex numbers specially
dtype = datatype(dset)
try
class_id = HDF5.h5t_get_class(dtype.id)
d = class_id == HDF5.H5T_COMPOUND ? read_complex(dtype, dset, T) : read(dset, T)
class_id = HDF5.API.h5t_get_class(dtype.id)
d = class_id == HDF5.API.H5T_COMPOUND ? read_complex(dtype, dset, T) : read(dset, T)
length(d) == 1 ? d[1] : d
finally
close(dtype)
Expand Down Expand Up @@ -208,9 +210,9 @@ function m_read(g::HDF5.Group)
T = str2type_matlab[mattype]
try
dtype = datatype(dset)
class_id = HDF5.h5t_get_class(dtype.id)
class_id = HDF5.API.h5t_get_class(dtype.id)
try
data = class_id == HDF5.H5T_COMPOUND ? read_complex(dtype, dset, T) : read(dset, T)
data = class_id == HDF5.API.H5T_COMPOUND ? read_complex(dtype, dset, T) : read(dset, T)
finally
close(dtype)
end
Expand Down Expand Up @@ -330,7 +332,7 @@ end
function m_writearray(parent::HDF5Parent, name::String, adata::AbstractArray{T}, compress::Bool) where {T<:HDF5BitsOrBool}
if compress
dset, dtype = create_dataset(parent, name, adata;
compress = 3, chunk = HDF5.heuristic_chunk(adata))
deflate = 3, chunk = HDF5.heuristic_chunk(adata))
else
dset, dtype = create_dataset(parent, name, adata)
end
Expand All @@ -350,7 +352,7 @@ function m_writearray(parent::HDF5Parent, name::String, adata::AbstractArray{Com
stype = dataspace(adata)
if compress
dset = create_dataset(parent, name, dtype, stype;
compress = 3, chunk = HDF5.heuristic_chunk(adata))
deflate = 3, chunk = HDF5.heuristic_chunk(adata))
else
dset = create_dataset(parent, name, dtype, stype)
end
Expand Down Expand Up @@ -599,19 +601,19 @@ end

## Utilities for handling complex numbers
function build_datatype_complex(T::Type)
memtype = create_datatype(HDF5.H5T_COMPOUND, 2*sizeof(T))
HDF5.h5t_insert(memtype, "real", 0, HDF5.hdf5_type_id(T))
HDF5.h5t_insert(memtype, "imag", sizeof(T), HDF5.hdf5_type_id(T))
memtype = create_datatype(HDF5.API.H5T_COMPOUND, 2*sizeof(T))
HDF5.API.h5t_insert(memtype, "real", 0, HDF5.hdf5_type_id(T))
HDF5.API.h5t_insert(memtype, "imag", sizeof(T), HDF5.hdf5_type_id(T))
return memtype
end

function check_datatype_complex(dtype::HDF5.Datatype)
n = HDF5.h5t_get_nmembers(dtype.id)
n = HDF5.API.h5t_get_nmembers(dtype.id)
if n != 2
return false
end
if HDF5.h5t_get_member_name(dtype.id, 0) != "real" ||
HDF5.h5t_get_member_name(dtype.id, 1) != "imag"
if HDF5.API.h5t_get_member_name(dtype.id, 0) != "real" ||
HDF5.API.h5t_get_member_name(dtype.id, 1) != "imag"
return false
end
true
Expand Down