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benhibou avatar benhibou commented on July 21, 2024

Alternatively, spec2nii works in one instance when instead of passing:

  • spec2nii bruker -m FID 6/fid which gave an error as specified above

one issues:

  • spec2nii bruker -m FID 6

where "6" is the directory containing the data. However in the other instance, in our case the "8" directory, issuing the command:

  • spec2nii bruker -m FID 8 results in the following error:
    spec2nii bruker -m FID 8/
    Traceback (most recent call last):
    File "/home/spectro/anaconda3/bin/spec2nii", line 10, in
    sys.exit(main())
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 666, in main
    spec2nii(*args)
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 283, in init
    args.func(args)
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 635, in bruker
    self.imageOut, self.fileoutNames = read_bruker(args)
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/spec2nii/bruker.py", line 44, in read_bruker
    for data, orientation, dwelltime, meta, name in yield_bruker(args):
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/spec2nii/bruker.py", line 94, in yield_bruker
    with dataset as d:
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 204, in enter
    self.load()
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 272, in load
    self.load_schema()
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 487, in load_schema
    self._schema = SchemaFid(self)
    File "/home/spectro/anaconda3/lib/python3.7/site-packages/brukerapi/schemas.py", line 73, in init
    raise MissingProperty(property)
    brukerapi.exceptions.MissingProperty: Dataset is missing the scheme_id property. We can offer some help, please contact us via https://github.com/isi-nmr/brukerapi-python

from brukerapi-python.

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