Writing data as a table in a hdf5 file.

I'm trying to write MATLAB data to an existing database of hdf5 files. Data in the database is currently being stored as table. The tables' columns can be different data types such as an integer or a string etc. and the columns also have labels like "longitude", "Name of patient" etc as a property of the table.

I think MATLAB's struct datatype is equivalent to the hdf5 table but I'm not sure how to save it. MATLAB says that the array is not numeric when I try to save the struct, DataStruct, in the example below.

h5write('h5testfile.h5', '/foo/Test', DataStruct);

Any ideas how I can fix this problem?

Answer 1

[John]

Only numeric data can be written with H5WRITE. In order to write table or compound data, you will need to use "formal" interfaces that wrap the HDF5 library API.

We provided the HDF Group with MATLAB versions of their own example codes that may help demonstrate how to do this. I would suggest that you go to http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-m.html and check out the compound data examples. Let me know how it goes.

[Simon]

Thanks. That example was quite helpful. We were able to create a compound file with our own data. Could you tell me how I'd have to change it to place the table within a number of subfolders inside the hdf5 file.

For example, inside the group '/foo/bar' or something like that? I tried

 plist = 'H5P_DEFAULT';
 foogroup = H5G.create(file,'foo',plist,plist,plist);
 bargroup = H5G.create(foogroup ,'bar',plist,plist,plist);

before the line

 dset = H5D.create (bargroup, DATASET, filetype, space, 'H5P_DEFAULT');

but it doesn't seem to create a valid h5 file.

[John]

I don't think I have enough information to tell what might be going wrong.

[per isakson]

See HDF5 MATLAB Examples