Skip to content

Crash when computing flats/darks using hdf5_entry = XXX

When using reconstructing from a NX file and a non-default entry (ex. hdf5_entry = entry0001) with flatfield = 1 (default), the NXFlatField class tries to load the flats/darks from the wrong location.

This suggests that the entry used is not propagated correctly.

Traceback (most recent call last):
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/bin/nabu", line 8, in <module>
    sys.exit(main())
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/app/reconstruct.py", line 88, in main
    proc = ProcessConfig(conf_dict=conf_dict, create_logger=logfile)
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/pipeline/processconfig.py", line 77, in __init__
    self._update_dataset_info_with_user_config()
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/pipeline/fullfield/processconfig.py", line 26, in _update_dataset_info_with_user_config
    update_dataset_info_flats_darks(
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/resources/nxflatfield.py", line 477, in update_dataset_info_flats_darks
    _get_flats_darks()
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/resources/nxflatfield.py", line 471, in _get_flats_darks
    if flatfield_mode != "force-compute" and processes_file is None and _load_flats_from_tomwer():
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/nabu/resources/nxflatfield.py", line 374, in _load_flats_from_tomwer
    new_flats = dataset_info.dataset_scanner.load_reduced_flats(return_as_url=True)
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/tomoscan/esrf/hdf5scan.py", line 1178, in load_reduced_flats
    return super().load_reduced_flats(
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/tomoscan/scanbase.py", line 1185, in load_reduced_flats
    return self._load_frame_dict(
  File "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/tomoscan/scanbase.py", line 1106, in _load_frame_dict
    dataset_or_group = h5s[data_path]
  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 "/scisoft/tomotools_env/nabu/ubuntu20.04/cuda10.1.243-3/ppc64le/nabu_dev/lib/python3.8/site-packages/h5py/_hl/group.py", line 288, 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 (component not found)'