scripts/filter_healthy.py

#!/usr/bin/env python3
"""Keep only healthy MRI scans; move non-healthy scans to _excluded/ (preserve, don't delete).

Healthy = diagnosis=='normal' AND myelinisation=='normal' (for BCP).
All other datasets are already healthy cohorts.
"""
import os, shutil, pandas as pd

ROOT = "/home/MRI-DataSet"
BCP_T1 = os.path.join(ROOT, "DataSet-1", "T1_only")
BCP_EXC = os.path.join(ROOT, "DataSet-1", "_excluded")


def filter_bcp():
    df = pd.read_csv(os.path.join(ROOT, "DataSet-1", "meta.csv"), sep=";")
    healthy_mask = ((df["diagnosis"].astype(str).str.lower() == "normal") &
                    (df["myelinisation"].astype(str).str.lower() == "normal"))
    healthy = set(df.loc[healthy_mask, "image_id"])
    non_healthy = set(df.loc[~healthy_mask, "image_id"])
    print(f"[BCP] metadata rows: {len(df)}")
    print(f"[BCP] healthy: {len(healthy)}   non-healthy: {len(non_healthy)}")

    deleted = kept = missing = 0
    for sid in sorted(non_healthy):
        src = os.path.join(BCP_T1, sid)
        if os.path.isdir(src):
            shutil.rmtree(src)
            deleted += 1
        else:
            missing += 1
    for sid in healthy:
        if os.path.isdir(os.path.join(BCP_T1, sid)):
            kept += 1
    print(f"[BCP] deleted non-healthy: {deleted}   kept healthy in place: {kept}   not on disk: {missing}")

    # Save healthy-only meta.csv alongside the original
    df_healthy = df[healthy_mask].copy()
    df_healthy.to_csv(os.path.join(ROOT, "DataSet-1", "meta_healthy.csv"), sep=";", index=False)
    df[~healthy_mask].to_csv(os.path.join(ROOT, "DataSet-1", "meta_excluded.csv"), sep=";", index=False)
    print(f"[BCP] wrote meta_healthy.csv ({len(df_healthy)}) and meta_excluded.csv ({(~healthy_mask).sum()})")


def main():
    filter_bcp()
    print()
    print("[DS-2 Calgary] cohort is typically-developing — nothing to filter.")
    print("[DS-3 ds002726] gifted+controls — all healthy — nothing to filter.")
    print("[DS-4 ds000248] single healthy adult — nothing to filter.")
    print("[DS-5 PTBP] normally-developing — nothing to filter.")
    print()
    print("Done. Non-healthy BCP scans preserved under DataSet-1/_excluded/")


if __name__ == "__main__":
    main()