I’m using Ubuntu 18.04.5 LTS with python 3.8.0 from apt. I created a fresh virtualenv and pip installed h5py for testing.
h5py version info:
>>> print(h5py.version.info)
Summary of the h5py configuration
---------------------------------
h5py 3.2.1
HDF5 1.12.0
Python 3.8.0 (default, Oct 28 2019, 16:14:01)
[GCC 8.3.0]
sys.platform linux
sys.maxsize 9223372036854775807
numpy 1.20.1
cython (built with) 0.29.22
numpy (built against) 1.17.5
HDF5 (built against) 1.12.0
I have a simple script where I’m trying to change the individual fields of a dataset.
import h5py
f = h5py.File('test.hdf5','w')
ds = f.create_dataset('test_dataset',1,dtype=[('a_float','<u8'),('a_string',h5py.string_dtype(encoding='utf-8'))])
ds[0] = (1, "some string")
test_float = 2
ds['a_float'] = test_float
assert ds[0][0] == test_float
test_string = "test string"
ds['a_string'] = test_string
In this script setting the float works as expected, but ds['a_string'] = test_string errors with:
Traceback (most recent call last):
File "/softdev/akuurstr/python/h5py_test.py", line 11, in <module>
ds['a_string'] = test_string
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/softdev/akuurstr/python/virtualenvs/h5py_test/lib/python3.8/site-packages/h5py/_hl/dataset.py", line 845, in __setitem__
val = val.view(numpy.dtype([(names[0], dtype)]))
File "/softdev/akuurstr/python/virtualenvs/h5py_test/lib/python3.8/site-packages/numpy/core/_internal.py", line 459, in _view_is_safe
raise TypeError("Cannot change data-type for object array.")
TypeError: Cannot change data-type for object array.
The only way I can set the dataset’s string is to replace the entire record. However it seems like I should be able to set the string field individually. I checked git issues but couldn’t find anything so I’m not sure if this is expected behaviour. Should I be posting this as a bug on git?