PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side files like .e.g excel sheets -- paper @JOSS https://doi.org/10.21105/joss.06067
Describe the bug
The following error occurs [in python] when attempting to use is_pet.pet_folder() on a folder containing DICOM-to-NIfTI transformed PET data:
To Reproduce
code/command used (copy/paste what you did)
from pathlib import Path
is_pet.pet_folder(Path(path/to/PET_NIFTI/folder))
error happening? (copy/paste the error)
Traceback (most recent call last):
File "./find_petdir.py", line 25, in <module>
print([str(folder) for folder in is_pet.pet_folder(Path(root).resolve())])
File "/usr/local/lib/python3.8/dist-packages/pypet2bids/is_pet.py", line 158, in pet_folder
files = read_files_in_parallel(all_files, pet_file, n_jobs=1, return_only_path=True)
File "/usr/local/lib/python3.8/dist-packages/pypet2bids/is_pet.py", line 61, in read_files_in_parallel
results = Parallel(n_jobs=n_jobs)(delayed(function)(file_path, **kwargs) for file_path in file_paths)
File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 1863, in __call__
return output if self.return_generator else list(output)
File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 1792, in _get_sequential_output
res = func(*args, **kwargs)
File "/usr/local/lib/python3.8/dist-packages/pypet2bids/is_pet.py", line 126, in pet_file
read_file = spread_sheet_check_for_pet(file_path)
File "/usr/local/lib/python3.8/dist-packages/pypet2bids/is_pet.py", line 26, in spread_sheet_check_for_pet
data = helper_functions.open_meta_data(sourcefile)
File "/usr/local/lib/python3.8/dist-packages/pypet2bids/helper_functions.py", line 406, in open_meta_data
metadata_dataframe = use_me_to_read(metadata_path, sep=separator)
TypeError: 'NoneType' object is not callable
Exception ignored in: <pypet2bids.is_pet.DummyFile object at 0x7ff53daedf70>
AttributeError: 'DummyFile' object has no attribute 'flush'
Expected behaviour
I was anticipating ispet to return the folder path. At the very least, this seems a bit restrictive, as using ispet on the individual PET NIfTI file itself doesn't produce an error, it simply returns nothing. Perhaps this is the expected behavior, but it would be nice if ispet could determine that the file is indeed PET, simply transformed to the NIfTi format.
Desktop (please complete the following information):
Describe the bug The following error occurs [in python] when attempting to use
is_pet.pet_folder()
on a folder containing DICOM-to-NIfTI transformed PET data:To Reproduce
Expected behaviour I was anticipating
ispet
to return the folder path. At the very least, this seems a bit restrictive, as usingispet
on the individual PET NIfTI file itself doesn't produce an error, it simply returns nothing. Perhaps this is the expected behavior, but it would be nice ifispet
could determine that the file is indeed PET, simply transformed to the NIfTi format.Desktop (please complete the following information):
1.2.10
(python)