Writing to compound dataset with variable length string via h5py (HDF5)

Question

I\'ve been able to create a compound dataset consisting of an unsigned int and a variable-length string in my HDF5 file using h5py, but I can\'t write to it.

Answer 1

Following on my earlier answer to Inexplicable behavior when using vlen with h5py

I ran this test (h5py version '2.2.1'):

In [4]: import h5py
In [5]: dt = h5py.special_dtype(vlen=str)
In [6]: f=h5py.File('foo.hdf5')
In [8]: ds1 = f.create_dataset('JustStrings',(10,), dtype=dt)
In [10]: ds1[0]='string'
In [11]: ds1[1]='a longer string'
In [13]: ds1[2:5]='one_string two_strings three'.split()

In [14]: ds1
Out[14]: <HDF5 dataset "JustStrings": shape (10,), type "|O4">

In [15]: ds1.value
Out[15]: 
array(['string', 'a longer string', 'one_string', 'two_strings', 'three',
       '', '', '', '', ''], dtype=object)

And for a mixed dtype like yours:

In [16]: ds2 = f.create_dataset('IntandStrings',(10,),
   dtype=np.dtype([("number",int),('astring',dt)]))
In [17]: ds2[0]=(1,'astring')
In [18]: ds2[1]=(10,'a longer string')
In [19]: ds2[2:4]=[(10,'a longer much string'),(0,'')]
In [20]: ds2.value
Out[20]: 
array([(1, 'astring'), (10, 'a longer string'),
       (10, 'a longer much string'), (0, ''), (0, ''), (0, ''), (0, ''),
       (0, ''), (0, ''), (0, '')], 
      dtype=[('number', '<i4'), ('astring', 'O')])

Trying to set a field by itself does not seem to work

ds2['astring'][4]='one two three four'

Instead I have to set the whole record:

ds2[4]=(123,'one two three four')

Trying to set the whole field produces the same error:

ds2['astring']='astring'

I initialed this dataset to (10,), while yours is (1,). But I think it's the same problem.

I can, though, set the whole numeric field:

In [48]: ds2['number']=np.arange(10)
In [50]: ds2['number']
Out[50]: array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
In [51]: ds2.value
Out[51]: 
array([(0, 'astring'), (1, 'a longer string'), 
       (2, 'a longer much string'),
       (3, ''), (4, 'one two three four'), (5, ''), 
       (6, ''), (7, ''),
       (8, ''), (9, '')], 
      dtype=[('number', '<i4'), ('astring', 'O')])