Re: [h5md-user] A note on the string type

[Peter Colberg]

On Fri, Dec 06, 2013 at 05:45:15PM +0100, Felix Höfling wrote:
> In conclusion, there seems to be a preference for fixed-length strings in
> h5py, but a preference for VL Strings in H5MD. Further, a novice user may
> easily mess up the string types, e.g., this issue is discussed in "Special
> topics" in the h5py manual ... not for beginners. This made me wondering
> again if forcing strings to be of VL type is a good idea, but I know that
> this is a majority opinion.

The novice user would probably store the wrong string type either way.

import h5py
f = h5py.File("/tmp/vlstring.h5", "w")
f.attrs["unit"] = "nm"
f.attrs["boundary"] = ["periodic", "periodic", "nonperiodic"]

HDF5 "vlstring.h5" {
GROUP "/" {
   ATTRIBUTE "boundary" {
      DATATYPE  H5T_STRING {
         STRSIZE 11;
         STRPAD H5T_STR_NULLPAD;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SIMPLE { ( 3 ) / ( 3 ) }
      DATA {
      (0): "periodic\000\000\000", "periodic\000\000\000", "nonperiodic"
      }
   }
   ATTRIBUTE "unit" {
      DATATYPE  H5T_STRING {
         STRSIZE H5T_VARIABLE;
         STRPAD H5T_STR_NULLTERM;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SCALAR
      DATA {
      (0): "nm"
      }
   }
}
}

For strings, h5py uses a variable-length string type. For arrays of
strings, h5py uses a fixed-length string type. Thus if you are a
novice user, better use pyh5md.

Peter