prep_adftd.py

"""ADFTD (OpenNeuro ds004504) preprocessing, following DL4mHealth/Medformer.

Steps (verbatim from Medformer's ADFTD_preprocessing.ipynb):
  * read the ASR/ICA-cleaned derivatives (.set, 19 channels, 500 Hz)
  * linear-interpolation resample 500 -> 256 Hz
  * segment into non-overlapping 256-timestamp windows, centred on the recording
  * label map {C: 0 healthy, F: 1 FTD, A: 2 AD}
Split (from Medformer's ADFTDLoader): subject-wise 60/20/20 within each class.
Normalisation: per-sample, per-channel standardisation (uea.normalize_batch_ts).
"""

import argparse
import os

import mne
import numpy as np
import pandas as pd
from scipy import interpolate

mne.set_log_level("ERROR")

LABEL_MAP = {"A": 2, "F": 1, "C": 0}


def resample(arr, freq=500, target=256):
    t = np.linspace(1, len(arr), len(arr))
    f = interpolate.interp1d(t, arr, kind="linear")
    t_new = np.linspace(1, len(arr), int(len(arr) / freq * target))
    return f(t_new)


def segment(mat, window=256):
    """mat: (T, C). Centre-anchored non-overlapping windows."""
    res = []
    start = mat.shape[0] // 2
    left = start - (start // window) * window
    right = start + ((mat.shape[0] - start) // window) * window
    for i in range(left, right, window):
        res.append(mat[i:i + window])
    return res


def main():
    ap = argparse.ArgumentParser()
    ap.add_argument("--root", default="data/ADFTD")
    ap.add_argument("--out", default="data/ADFTD/processed")
    ap.add_argument("--window", type=int, default=256)
    args = ap.parse_args()

    parts = pd.read_csv(os.path.join(args.root, "participants.tsv"), sep="\t")
    labels = {}
    for row in parts.values:
        pid = int(str(row[0])[-3:])
        labels[pid] = LABEL_MAP[row[3]]

    deriv = os.path.join(args.root, "derivatives")
    feats, ys, subs = [], [], []
    for pid in sorted(labels):
        path = os.path.join(deriv, f"sub-{pid:03d}", "eeg",
                            f"sub-{pid:03d}_task-eyesclosed_eeg.set")
        raw = mne.io.read_raw_eeglab(path, preload=True)
        sig = raw.get_data()  # (C, T) at 500 Hz
        res = np.stack([resample(sig[c]) for c in range(sig.shape[0])], axis=1)  # (T', C)
        for win in segment(res, args.window):
            feats.append(win.astype(np.float32))
            ys.append(labels[pid])
            subs.append(pid)
        print(f"sub-{pid:03d} label={labels[pid]} raw={sig.shape} "
              f"resampled={res.shape} windows={len(segment(res, args.window))}", flush=True)

    X = np.stack(feats)                      # (N, 256, 19)
    y = np.array(ys, dtype=np.int64)
    s = np.array(subs, dtype=np.int64)
    print("total", X.shape, np.bincount(y))

    # subject-wise 60/20/20 within each class (Medformer ADFTDLoader, a=0.6, b=0.8)
    train_ids, val_ids, test_ids = [], [], []
    for cls in (0, 1, 2):
        ids = sorted([p for p in labels if labels[p] == cls])
        a, b = int(0.6 * len(ids)), int(0.8 * len(ids))
        train_ids += ids[:a]
        val_ids += ids[a:b]
        test_ids += ids[b:]
    print("subjects train/val/test:", len(train_ids), len(val_ids), len(test_ids))

    os.makedirs(args.out, exist_ok=True)
    for name, ids in (("train", train_ids), ("val", val_ids), ("test", test_ids)):
        m = np.isin(s, ids)
        Xi = X[m]
        mu = Xi.mean(axis=1, keepdims=True)
        sd = Xi.std(axis=1, keepdims=True)
        sd[sd == 0] = 1.0
        Xi = ((Xi - mu) / sd).astype(np.float32)
        np.save(os.path.join(args.out, f"X_{name}.npy"), Xi)
        np.save(os.path.join(args.out, f"y_{name}.npy"), y[m])
        np.save(os.path.join(args.out, f"subj_{name}.npy"), s[m])
        print(name, Xi.shape, np.bincount(y[m]))


if __name__ == "__main__":
    main()