Storing string datasets in hdf5 with unicode - python-3.x

Question

I am trying to store variable string expressions from a file which contains special characters, like ø, æ , and å. Here is my code:
import h5py as h5
file = h5.File('deleteme.hdf5','a')
dt = h5.special_dtype(vlen=str)
dset = file.create_dataset("text",(1,),dtype=dt)
dset.attrs[str(1)] = "some text with ø, æ, å"
However the text is not stored properly. The data stored contains text:
"some text with \37777777703\37777777670, \37777777703\37777777646,\37777777703\37777777645"
How can I store the special characters properly? I have tried to follow the guide provided in the documentation here: Strings in HDF5 - Variable-length UTF-8
Edit:
The output was from h5dump. The answer below verified that the characters are properly stored as utf-8.

Answer 1

With:
import numpy as np
import h5py as h5
file = h5.File('deleteme.hdf5','w')
dt = h5.special_dtype(vlen=str)
dset = file.create_dataset("text",(3,),dtype=dt)
dset[:] = 'ø æ å'.split()
dset.attrs["1"] = "some text with ø, æ, å"
file.close()
file = h5.File('deleteme.hdf5','r')
print(file['text'][:])
print(file['text'].attrs["1"])
file.close()
I see:
$ python3 stack44661467.py
['ø' 'æ' 'å']
some text with ø, æ, å
That is h5py does see/interpret the strings as unicode - writing and reading.
With the dump utility:
$ h5dump deleteme.hdf5
HDF5 "deleteme.hdf5" {
GROUP "/" {
DATASET "text" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 3 ) / ( 3 ) }
DATA {
(0): "\37777777703\37777777670", "\37777777703\37777777646",
(2): "\37777777703\37777777645"
}
ATTRIBUTE "1" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "some text with \37777777703\37777777670, \37777777703\37777777646, \37777777703\37777777645"
}
}
}
}
}
Note that in both case the datatype is marked UTF8
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
That's what the docs say:
http://docs.h5py.org/en/latest/strings.html#variable-length-utf-8
They can store any character a Python unicode string can store, with the exception of NULLs. In the file these are created as variable-length strings with character set H5T_CSET_UTF8.
Let h5py (or other reader) worry about interpreting \37777777703\37777777670 as the proper unicode character.

Answer 2

You should try storing your data in UTF-8 format by doing the following:
To encode in utf-8 format (before storingwith h5py) do:
u"æ".encode("utf-8")
which returns:
'\xc3\xa6'
Then to decode you could use the string decode like this:
'\xc3\xa6'.decode("utf-8")
which would return:
æ
Hope it helps!
EDIT
When you open files and you want them to be in utf-8, you can use the encoding parameter on the read file method:
f = open(fname, encoding="utf-8")
This should help properly encoding the original file.
Source: python-notes