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

Package:
python3-fabio
Source:
python-fabio
Description:
I/O library for images produced by 2D X-ray detector - Python3
Submitter:
Martin Lutz
Date:
2021-05-10 06:15:04 UTC
Severity:
normal
#920257#5
Date:
2019-01-23 10:43:29 UTC
From:
To:
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:
['entry']
['data', 'definition', 'end_time', 'instrument', 'sample', 'start_time']
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)"
#920257#10
Date:
2019-01-23 19:49:25 UTC
From:
To:
Hello, here an answer from the ESRF.
#920257#15
Date:
2019-01-23 19:57:47 UTC
From:
To:
Hi,

The structure of the dataset in the file is "entry/data/data_000001",
not "entry/data_000001".

Moreover the bug you reported should be in h5py, not fabio as you don't
use fabio in your code snippet.

This bug has probably nothing to do the debian packaging, so it is
probably better to discuss with the development bug-tacker:
https://github.com/silx-kit/fabio/issues

Cheers,

Jérôme (also maitainer for fabio over the last decade)
#920257#20
Date:
2019-01-28 15:39:12 UTC
From:
To:
Hey,

I do not know what is the best place for discussion. Please decide...

The program fabio_viewer fails on this dataset with:
Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/fabio/app/viewer.py", line 222,
in open_h5_data_series
     entry = nxs.get_entries()[0]
IndexError: list index out of range
Aborted

Best wishes,
Martin



On Wed, 23 Jan 2019 20:57:47 +0100 =?UTF-8?B?SsOpcsO0bWU=?= Kieffer  <jerome.kieffer@terre-adelie.org> wrote:

 > Hi,
 >
 > The structure of the dataset in the file is "entry/data/data_000001",
 > not "entry/data_000001".
 >
 > Moreover the bug you reported should be in h5py, not fabio as you don't
 > use fabio in your code snippet.
 >
 > This bug has probably nothing to do the debian packaging, so it is
 > probably better to discuss with the development bug-tacker:
 > https://github.com/silx-kit/fabio/issues
 >
 > Cheers,
 >
 > Jérôme (also maitainer for fabio over the last decade)
 >
 >
#920257#25
Date:
2020-04-04 08:24:51 UTC
From:
To:
Can you check if this is still an issue with the latest version
available in buster-backports ?

thanks
#920257#30
Date:
2021-05-10 06:04:17 UTC
From:
To:
I confirm the master-file can properly be read by FabIO (tested today with the master branch).
The data files cannot be loaded individually, their structure do not look like genuine Dectris files.