CT/lung/src/preprocessing/dicom_to_nifti.py

from __future__ import annotations

import argparse
from pathlib import Path


def convert_dicom_series(input_dir: str | Path, output_path: str | Path) -> Path:
    """Convert one DICOM series directory to NIfTI using SimpleITK."""

    try:
        import SimpleITK as sitk
    except ImportError as exc:
        raise ImportError("SimpleITK is required for DICOM to NIfTI conversion") from exc

    input_dir = Path(input_dir)
    output_path = Path(output_path)
    reader = sitk.ImageSeriesReader()
    series_ids = reader.GetGDCMSeriesIDs(str(input_dir))
    if not series_ids:
        raise ValueError(f"No DICOM series found in {input_dir}")
    files = reader.GetGDCMSeriesFileNames(str(input_dir), series_ids[0])
    reader.SetFileNames(files)
    image = reader.Execute()
    output_path.parent.mkdir(parents=True, exist_ok=True)
    sitk.WriteImage(image, str(output_path))
    return output_path


def main() -> None:
    parser = argparse.ArgumentParser(description="Convert one DICOM series folder to NIfTI.")
    parser.add_argument("--input-dir", required=True)
    parser.add_argument("--output", required=True)
    args = parser.parse_args()
    convert_dicom_series(args.input_dir, args.output)


if __name__ == "__main__":
    main()