Modify DICOM files

modify_dicoms.py

import argparse
import os
import pydicom
from pathlib import Path

parser = argparse.ArgumentParser()
parser.add_argument('input_folder', help='The DICOM input folder.')
parser.add_argument('output_folder', help='The DICOM output folder.')
parser.add_argument('-m', '--modify_dicom_tag', help='Modifies a DICOM tag.', type=str, nargs=2, action='append')

args = parser.parse_args()    

modalities = []
for root, dirs, files in os.walk(args.input_folder):
    for file in files:
        filepath = os.path.join(root, file)
        ds = pydicom.dcmread(filepath)
        modalities.append(ds.Modality)

modalities = ','.join(list(set(modalities)))

for root, dirs, files in os.walk(args.input_folder):
    for file in files:
        filepath = os.path.join(root, file)
        ds = pydicom.dcmread(filepath)
        if args.modify_dicom_tag:
            for modification in args.modify_dicom_tag:
                tag_to_modify = modification[0]
                value_to_assign = modification[1]
                ds[tag_to_modify].value = value_to_assign
        patient_id = ds.PatientID
        study_name = f'{ds.StudyDate}_{ds.StudyTime}_{modalities}'   
        series_descr = ds.SeriesDescription
        outpath = os.path.join(args.output_folder, patient_id, study_name, series_descr)
        Path(outpath).mkdir(parents=True, exist_ok=True)
        ds.save_as(os.path.join(outpath, file))