CT/lung2/scripts/clean_radiomics.py

from __future__ import annotations

import argparse
import sys
from pathlib import Path

ROOT = Path(__file__).resolve().parents[1]
if str(ROOT) not in sys.path:
    sys.path.insert(0, str(ROOT))

import pandas as pd

from src.features.radiomics import clean_radiomics_matrix
from src.utils import ensure_dir, load_config


def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("--config", default="configs/tcga_lgg_qc.yaml")
    args = parser.parse_args()
    cfg = load_config(args.config)
    processed = Path(cfg["paths"]["processed_dir"])
    raw = processed / "radiomics_raw.csv"
    if not raw.exists():
        raise FileNotFoundError(f"missing radiomics file: {raw}")
    cleaned = clean_radiomics_matrix(
        pd.read_csv(raw),
        missing_threshold=cfg["radiomics"]["missing_threshold"],
        correlation_threshold=cfg["radiomics"]["correlation_threshold"],
    )
    out = processed / "radiomics_clean.csv"
    ensure_dir(processed)
    cleaned.to_csv(out, index=False)
    print(f"wrote {out} with {cleaned.shape[1] - 1} features")


if __name__ == "__main__":
    main()