pre/code/download.py

"""Download the dataset from HuggingFace, unzip, and build a case manifest.

Usage:
    python -m toothcanal.download --config configs/default.yaml

On AutoDL (China) you may want a mirror:
    export HF_ENDPOINT=https://hf-mirror.com
"""
import os, glob, zipfile, argparse, re
from .utils import load_config, ensure_dir, numeric_id, write_json


def _safe_extract(zip_path, dest):
    """Extract a zip, fixing common CJK filename mojibake (cp437 -> gbk/utf-8)."""
    with zipfile.ZipFile(zip_path) as zf:
        for info in zf.infolist():
            name = info.filename
            raw = name.encode("cp437", errors="ignore")
            for enc in ("gbk", "utf-8"):
                try:
                    name = raw.decode(enc)
                    break
                except Exception:
                    continue
            target = os.path.join(dest, name)
            if info.is_dir() or name.endswith("/"):
                ensure_dir(target)
                continue
            ensure_dir(os.path.dirname(target))
            with zf.open(info) as src, open(target, "wb") as out:
                out.write(src.read())


def download_and_extract(cfg, only_substrings=None):
    from huggingface_hub import HfApi, hf_hub_download
    repo = cfg["paths"]["hf_repo"]
    raw_dir = ensure_dir(cfg["paths"]["raw_dir"])

    api = HfApi()
    files = api.list_repo_files(repo_id=repo, repo_type="dataset")
    zips = [f for f in files if f.lower().endswith(".zip")]
    skips = cfg["paths"].get("skip_zip_substrings", [])
    zips = [f for f in zips if not any(s in f for s in skips)]
    if only_substrings:
        zips = [f for f in zips if any(s in f for s in only_substrings)]
    print(f"[download] using {len(zips)} zip files (skipped {skips}, only={only_substrings}): {zips}")

    for zf in zips:
        print(f"[download] fetching {zf} ...")
        local = hf_hub_download(repo_id=repo, repo_type="dataset", filename=zf,
                                local_dir=os.path.join(raw_dir, "_zips"))
        print(f"[download] extracting {os.path.basename(local)} ...")
        _safe_extract(local, raw_dir)
    return raw_dir


def _build_image_from_dicom(folder):
    """Read all *.dcm in `folder`, write image_from_dicom.nii.gz, return its path."""
    import SimpleITK as sitk, glob as _g
    dcm_files = sorted(_g.glob(os.path.join(folder, "*.dcm")))
    if len(dcm_files) < 8:
        return None
    reader = sitk.ImageSeriesReader()
    try:
        ids = reader.GetGDCMSeriesIDs(folder)
        if ids:
            # pick the largest series (most slices)
            best_files, best_n = None, -1
            for sid in ids:
                fnames = reader.GetGDCMSeriesFileNames(folder, sid)
                if len(fnames) > best_n:
                    best_n, best_files = len(fnames), fnames
            reader.SetFileNames(best_files)
        else:
            reader.SetFileNames(dcm_files)
        img = reader.Execute()
    except Exception:
        return None
    out = os.path.join(folder, "image_from_dicom.nii.gz")
    sitk.WriteImage(img, out)
    return out


def _pick_label_in(folder):
    """Among nii.gz files in `folder` (excluding image_from_dicom), pick the most
    likely label: prefer the canonical filename if present, else the LARGEST file
    (the duplicate 01.nii.gz / 31.nii.gz pair are usually the same content, but
    sometimes 01.nii.gz is a symlink/older copy)."""
    canonical = os.path.join(folder, "zzz21_tooth_mask_3ik3_label_adjust.nii.gz")
    if os.path.exists(canonical):
        return canonical
    cands = [p for p in glob.glob(os.path.join(folder, "*.nii.gz"))
             if os.path.basename(p) != "image_from_dicom.nii.gz"]
    if not cands:
        return None
    # follow symlinks; pick the one with the largest real size
    return max(cands, key=lambda p: os.path.getsize(os.path.realpath(p)))


def _series_uid_dir_to_case_name(folder, raw_dir):
    """Pick the case-folder name by scanning relpath segments. The DEEPEST segment
    that is purely numeric (optionally followed by trailing dashes) and in 1..40
    is the case folder. Earlier batch folders like '1-20' are NOT pure-numeric
    (they contain a dash between two digits) so they won't match `\\d+-*`."""
    rel = os.path.relpath(folder, raw_dir).split(os.sep)
    chosen = None
    for seg in rel:
        m = re.fullmatch(r"0*(\d+)-*", seg)
        if m and 1 <= int(m.group(1)) <= 40:
            chosen = seg
    return chosen or os.path.basename(os.path.dirname(folder))


def _find_label_for(folder, raw_dir, case_num):
    """Look for the label .nii.gz file for this case. Strategy:
       1. Same folder as the DICOMs.
       2. Walk up to the CASE folder (whose name starts with case_num) and
          search every .nii.gz inside it (excluding image_from_dicom).
       3. If still nothing, look in sibling 'case/' summary folders one level
          up from the case (e.g. data/raw/21-30/21-30/zzz027.nii.gz).
    """
    canonical = "zzz21_tooth_mask_3ik3_label_adjust.nii.gz"

    def _ok(p):
        return os.path.basename(p) != "image_from_dicom.nii.gz"

    # 1. same folder
    here = [p for p in glob.glob(os.path.join(folder, "*.nii.gz")) if _ok(p)]
    if here:
        return max(here, key=lambda p: os.path.getsize(os.path.realpath(p)))

    # 2. walk up to the case folder
    cur = folder
    while True:
        parent = os.path.dirname(cur)
        if parent == raw_dir or parent == cur:
            break
        cur = parent
        m = re.match(r"0*(\d+)", os.path.basename(cur))
        if m and int(m.group(1)) == case_num:
            cands = [p for p in glob.glob(os.path.join(cur, "**", "*.nii.gz"),
                                          recursive=True) if _ok(p)]
            if cands:
                # prefer one whose filename contains the case number
                preferred = [p for p in cands if str(case_num) in os.path.basename(p)
                             or canonical in os.path.basename(p)]
                pool = preferred or cands
                return max(pool, key=lambda p: os.path.getsize(os.path.realpath(p)))
            break
    return None


def discover_cases(raw_dir):
    """Find all CBCT cases under raw_dir. A case = the directory directly
    containing the DICOM slices (>=8 .dcm files), OR a directory with an
    explicit image_from_dicom.nii.gz. Labels are searched in the same folder,
    then up the directory tree to the case-numbered ancestor."""
    cases = {}
    explicit_imgs = glob.glob(os.path.join(raw_dir, "**", "image_from_dicom.nii.gz"),
                              recursive=True)
    candidate_dirs = set()
    for p in explicit_imgs:
        candidate_dirs.add(os.path.dirname(p))
    # any directory with >=8 .dcm files is a DICOM series
    for folder, dirs, files in os.walk(raw_dir):
        # skip hidden and the HF cache
        parts = folder.split(os.sep)
        if any(seg.startswith(".") or seg == "_zips" for seg in parts):
            dirs[:] = []
            continue
        n_dcm = sum(1 for f in files if f.lower().endswith(".dcm"))
        if n_dcm >= 8:
            candidate_dirs.add(folder)

    for folder in sorted(candidate_dirs):
        # derive a stable case id and a numeric case number from the path.
        # The path may look like  raw/1-20/01-/20230519/<series_uid>/  so the FIRST
        # segment with a number (`1-20`) is the batch folder, not the case. We want
        # the DEEPEST segment whose name parses as a single number in 1..40 — that's
        # the actual case folder.
        rel = os.path.relpath(folder, raw_dir).split(os.sep)
        case_num = -1
        case_name = None
        for seg in rel:
            m = re.fullmatch(r"0*(\d+)-*", seg)        # purely numeric + trailing dashes
            if m and 1 <= int(m.group(1)) <= 40:
                case_num = int(m.group(1))
                case_name = seg                        # keep updating -> deepest wins
        if case_num < 0:
            print(f"[discover] cannot infer case number from {folder}; skipping")
            continue

        # if multiple series exist under the same case (rare here), keep only the
        # largest one (most DICOM slices)
        prev = cases.get(case_name)
        n_dcm = sum(1 for f in os.listdir(folder) if f.lower().endswith(".dcm"))
        if prev is not None and prev.get("n_dcm", 0) >= n_dcm and prev.get("has_real_dcm", True):
            continue

        # build image_from_dicom if not already present
        img_path = os.path.join(folder, "image_from_dicom.nii.gz")
        if not os.path.exists(img_path):
            if n_dcm >= 8:
                print(f"[discover] {case_name}: building image_from_dicom.nii.gz "
                      f"from {n_dcm} DICOM slices in {folder} ...")
                built = _build_image_from_dicom(folder)
                if built is None:
                    print(f"[discover] {folder}: DICOM read failed, skipping.")
                    continue
                img_path = built
            else:
                continue

        label = _find_label_for(folder, raw_dir, case_num)
        if label is None:
            print(f"[discover] {case_name}: no label .nii.gz found anywhere in "
                  f"its subtree, skipping.")
            continue
        cases[case_name] = dict(image=img_path, label=label, num=case_num,
                                n_dcm=n_dcm, has_real_dcm=True)

    cases = {k: {kk: vv for kk, vv in v.items() if kk not in ("n_dcm", "has_real_dcm")}
             for k, v in sorted(cases.items(), key=lambda kv: kv[1]["num"])}
    print(f"[discover] found {len(cases)} cases: {[c for c in cases]}")
    return cases


def main():
    ap = argparse.ArgumentParser()
    ap.add_argument("--config", default="configs/default.yaml")
    ap.add_argument("--skip_download", action="store_true",
                    help="only (re)build manifest from already-extracted raw_dir")
    ap.add_argument("--only_zips", nargs="*", default=None,
                    help="only fetch zips whose name contains any of these substrings "
                         "(e.g. --only_zips 31-35   for the smoke test)")
    args = ap.parse_args()
    cfg = load_config(args.config)

    if not args.skip_download:
        download_and_extract(cfg, only_substrings=args.only_zips)

    cases = discover_cases(cfg["paths"]["raw_dir"])
    if not cases:
        raise SystemExit("No cases found. Check raw_dir / extraction.")
    write_json(cases, os.path.join(cfg["paths"]["raw_dir"], "manifest.json"))
    print(f"[download] manifest written with {len(cases)} cases.")


if __name__ == "__main__":
    main()