How to write a numeric attribute as array size scalar to HDF5 files using high level MATLAB HDF5 functions?

I'm writing scalar attributes to a HDF5 file using the MATLAB high level functions. This works well for string type attribute values but for integer or floating point attribute values always result in array size 1 , not in array size scalar. (See figure)

Question: Some of the HDF5 reading tools I use are strict on this format definitions and require scalars. How can I force the HDF5 high level functions to set the array size information in the file to scalar instead of 1 ?

Example code :

Assign value to attribute variable:

aTestField=int32(16);

Check if this is a scalar, this returns 1.

isscalar(aTestField)

Write the attribute to my file:

h5writeatt( myFile,'/','aTestField', aTestField);

However, the result in HDF5 file is array size 1.

Answer 1

[Chenghang Zhang]

h5writeatt doesn't offer lots of options. Use these guys:

fid = H5F.open([hdf5_file],'H5F_ACC_RDWR','H5P_DEFAULT');
gid = H5G.open(fid,"/*/*"); %specify the location of the attribute
typeID = H5T.copy("H5T_NATIVE_INT32"); %see https://api.h5py.org/h5t.html for more options
spaceID = H5S.create("H5S_SCALAR"); %specify it as a scalar
acpl = H5P.create("H5P_ATTRIBUTE_CREATE");
attrID = H5A.create(gid,"attr_name",typeID,spaceID,acpl);
H5A.write(attrID,"H5ML_DEFAULT",attr_value);

%Close everything
H5A.close(attrID);
H5S.close(spaceID);
H5T.close(typeID);
H5F.close(fid);
H5G.close(gid);
H5P.close(acpl);

[Haite van der Schaaf]

Thank you ! This does the trick !

Answer 2

[gts]

Hi there,

You may consider the following fix of the MATLAB original 'h5writeatt.m' function. Replace the createDataspaceId function with the function provided below. Note that the fix adds a 'isscalar' check for the attribute and create a scalar dataspace instead of calling ‘H5S.create_simple’, which covers the matrix cases. In the original 'h5writeatt.m' there was no distinction for a scalar case, so it was treated as a matrix.

Hope this helps,

George

function dataspace_id = createDataspaceId(attvalue)

% Setup the dataspace ID. This just depends on how many elements the

% attribute actually has.

if isempty(attvalue)

dataspace_id = H5S.create('H5S_NULL');

return;

elseif ischar(attvalue)

if isrow(attvalue)

dataspace_id = H5S.create('H5S_SCALAR');

return

else

error(message('MATLAB:imagesci:h5writeatt:badStringSize'));

end

else

if isscalar(attvalue)

dataspace_id = H5S.create('H5S_SCALAR');

elseif ismatrix(attvalue) && ( any(size(attvalue) ==1) )

rank = 1;

dims = numel(attvalue);

dataspace_id = H5S.create_simple(rank ,dims,dims);

else

% attribute is a "real" 2D value.

rank = ndims(attvalue);

dims = fliplr(size(attvalue));

dataspace_id = H5S.create_simple(rank, dims, dims);

end

end