| |
| """Fill empty patient IDs of a metadata export by grouping on identifying columns.""" |
|
|
| import argparse |
|
|
| from auto_detect_breast_mri.config import column |
| from auto_detect_breast_mri.data.metadata import fill_nan_id_values_by_group |
|
|
|
|
| def main(): |
| """ |
| Fill missing patient IDs of a metadata export by grouping on identifying columns. |
| |
| The file to work on must be given explicitly; there are no built in paths: |
| |
| python scripts/data_utils/fill_missing_patient_ids.py <data_file.xlsx> <sheet> \ |
| --id-column PNR --grouping Firstname Lastname Birthdate --backup-table <metadata.csv> |
| """ |
| parser = argparse.ArgumentParser(description="Fill empty patient IDs in a metadata export.") |
| parser.add_argument("data_file", help="metadata export (.xlsx) to fill in place") |
| parser.add_argument("sheet", help="name of the sheet holding the ID and grouping columns") |
| parser.add_argument("--id-column", default=None, |
| help="name of the patient ID column. Default: the configured patient_id column") |
| parser.add_argument("--grouping", nargs="+", required=True, |
| help="columns that identify a patient, e.g. Firstname Lastname Birthdate") |
| parser.add_argument("--backup-table", default=None, |
| help="optional second table to take IDs from") |
| args = parser.parse_args() |
|
|
| fill_nan_id_values_by_group(args.data_file, args.sheet, |
| args.id_column or column("patient_id"), |
| args.grouping, args.backup_table) |
|
|
|
|
| if __name__ == '__main__': |
| main() |
|
|
