Bug#920257: python3-fabio: program fails with Nexus data from Diamond Light Source

[Martin Lutz]

Package: python3-fabio
Version: 0.8.0+dfsg-1
Severity: normal

Dear Maintainer,

I have tried to reproduce the hdf5 example from the fabio manual on data from
the Diamond Light Source and ran into errors. The data can be obtained from
https://zenodo.org/record/2529979#.XEhDGpwo_zJ

This is what I did:

>>> import fabio, h5py
>>> h5_file = h5py.File("thaumatin_9_1_master.h5")
>>> print(list(h5_file.keys()))
['entry']

>>> print(list(h5_file["entry"].keys()))
['data', 'definition', 'end_time', 'instrument', 'sample', 'start_time']

>>> print(h5_file["entry/data_000001"].shape)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  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 "/usr/lib/python3/dist-packages/h5py/_hl/group.py", line 177, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  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 "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'data_000001' doesn't exist)"


-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages python3-fabio depends on:
ii  libc6                               2.28-5
ii  python3                             3.7.1-3
ii  python3-h5py                        2.8.0-3
ii  python3-lxml                        4.3.0-1
ii  python3-matplotlib                  3.0.2-2
ii  python3-numpy [python3-numpy-abi9]  1:1.16.0-1
ii  python3-pil                         5.4.1-1
ii  python3-pkg-resources               40.6.3-1
ii  python3-pyqt5                       5.11.3+dfsg-1+b3
ii  python3-six                         1.12.0-1

python3-fabio recommends no packages.

Versions of packages python3-fabio suggests:
pn  python-fabio-doc  <none>

-- no debconf information