nipoppy.workflows.dicom_reorg.DicomReorgWorkflow¶

class nipoppy.workflows.dicom_reorg.DicomReorgWorkflow(dpath_root, copy_files=False, check_dicoms=False, fpath_layout=None, verbose=False, dry_run=False)¶

Workflow for organizing raw DICOM files.

Parameters:

dpath_root (nipoppy.env.StrOrPathLike)
copy_files (bool)
check_dicoms (bool)
fpath_layout (Optional[nipoppy.env.StrOrPathLike])
verbose (bool)
dry_run (bool)

apply_fname_mapping(fpath_source, participant_id, session_id)¶

Apply a mapping from the original (full) file path to destination file name.

Prepend a short hash of the path to avoid filename collisions across DICOM series, while ensuring short filenames in nested directory structures.

Parameters:

fpath_source (nipoppy.env.StrOrPathLike)
participant_id (str)
session_id (str)

Return type:

str

get_fpaths_to_reorg(participant_id, session_id)¶

Get file paths to reorganize for a single participant and session.

Parameters:

participant_id (str)
session_id (str)

Return type:

list[pathlib.Path]

get_participants_sessions_to_run()¶: Return participant-session pairs to reorganize.

run_cleanup()¶

Clean up after main DICOM reorg part is run.

Specifically: - Write updated curation status file - Log a summary message

run_main()¶: Reorganize all downloaded DICOM files.

run_setup()¶: Update the curation status table in case it is not up-to-date.

run_single(participant_id, session_id)¶

Reorganize downloaded DICOM files for a single participant and session.

Parameters:

participant_id (str)
session_id (str)

check_dicoms = False¶

copy_files = False¶

n_success = 0¶

n_total = 0¶