Open-Minds-Lab / mrQA

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
https://open-minds-lab.github.io/mrQA/
Apache License 2.0
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--style dicom is not listed as an option #21

Closed yarikoptic closed 1 year ago

yarikoptic commented 1 year ago

"impossible" to figure out -- please add --version:

bids@rolando:/inbox/BIDS/Wager/Wager/1076_spacetop$ ~/.local/bin/mr_proto_compl --version
usage: mr_proto_compl -d DATA_ROOT [-o OUTPUT_DIR] [-s STYLE] [-n NAME] [-h] [-r] [-v] [-ref REFERENCE_PATH] [--strategy STRATEGY] [--include_phantom] [--metadata_root METADATA_ROOT] [-l LOGGING] [--skip SKIP [SKIP ...]]
mr_proto_compl: error: the following arguments are required: -d/--data_root
bids@rolando:/inbox/BIDS/Wager/Wager/1076_spacetop$ ~/.local/bin/mr_proto_compl --help | grep -A1 -e '-s STYLE,'
  -s STYLE, --style STYLE
                        type of dataset, one of [xnat|bids|other]

So - no dicom is given as an option at all.

Moreover that intriguing `other` I am not sure what it is about ```shell bids@rolando:/inbox/BIDS/Wager/Wager/1076_spacetop$ ~/.local/bin/mr_proto_compl --data_root ./sourcedata/sub-0001/ses-01/ --output_dir .heudiconv/mrQA --style other /home/bids/singularity_home/.local/lib/python3.9/site-packages/mrQA/cli.py:84: UserWarning: Expected a unique identifier for caching data. Got NoneType. Using a random name. Use --name flag for persistent metadata dataset = import_dataset(data_root=args.data_root, Traceback (most recent call last): File "/home/bids/singularity_home/.local/bin/mr_proto_compl", line 8, in sys.exit(main()) File "/home/bids/singularity_home/.local/lib/python3.9/site-packages/mrQA/cli.py", line 84, in main dataset = import_dataset(data_root=args.data_root, File "/home/bids/singularity_home/.local/lib/python3.9/site-packages/MRdataset/base.py", line 81, in import_dataset dataset_class = find_dataset_using_style(style.lower()) File "/home/bids/singularity_home/.local/lib/python3.9/site-packages/MRdataset/base.py", line 113, in find_dataset_using_style dataset_lib = importlib.import_module(dataset_modulename) File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 984, in _find_and_load_unlocked ModuleNotFoundError: No module named 'MRdataset.other_dataset' ```
raamana commented 1 year ago

thanks yarik for this great testing and detailed reports. We will look into and fix this asap. Sorry to get you to run into basis issues - we will up our testing to the best of our abilities.

sinhaharsh commented 1 year ago

The issue has been fixed. Although the option is called --format now.