| """Image-ONLY preprocessing for pure-CBCT inference (NO ground-truth labels).""" |
| import os, glob, argparse |
| import numpy as np |
| from tqdm import tqdm |
| from .utils import load_config, ensure_dir, load_nii, resample_to_spacing |
|
|
|
|
| def _normalize_image(img, clip): |
| img = np.clip(img, clip[0], clip[1]).astype(np.float32) |
| lo, hi = float(img.min()), float(img.max()) |
| if hi - lo < 1e-5: |
| return np.zeros_like(img) |
| return (img - lo) / (hi - lo) |
|
|
|
|
| def discover_images(raw_dir): |
| cases = {} |
| for p in glob.glob(os.path.join(raw_dir, "**", "image_from_dicom.nii.gz"), |
| recursive=True): |
| case = os.path.basename(os.path.dirname(p)) |
| cases[case] = p |
| return dict(sorted(cases.items())) |
|
|
|
|
| def process_image_only(cid, image_path, cfg): |
| pp = cfg["preprocess"] |
| img, imeta = load_nii(image_path) |
| img, imeta = resample_to_spacing(img, imeta, pp["spacing"], is_label=False) |
| img = _normalize_image(img, pp["clip_hu"]) |
| z = np.zeros(img.shape, dtype=np.uint8) |
| out_dir = ensure_dir(cfg["paths"]["proc_dir"]) |
| np.savez_compressed( |
| os.path.join(out_dir, f"{cid}.npz"), |
| image=img.astype(np.float32), |
| sem=z, inst=z, cinst=z, desc=z, |
| spacing=np.array(imeta["spacing"], dtype=np.float32), |
| origin=np.array(imeta["origin"], dtype=np.float32), |
| n_instances=0, |
| ) |
| return dict(case=cid, shape=list(img.shape)) |
|
|
|
|
| def main(): |
| ap = argparse.ArgumentParser() |
| ap.add_argument("--config", default="configs/cbct_only.yaml") |
| ap.add_argument("--raw", default=None, |
| help="folder to scan for image_from_dicom.nii.gz (default: paths.raw_dir)") |
| ap.add_argument("--force", action="store_true") |
| args = ap.parse_args() |
| cfg = load_config(args.config) |
|
|
| raw_dir = args.raw or cfg["paths"]["raw_dir"] |
| cases = discover_images(raw_dir) |
| if not cases: |
| raise SystemExit(f"No image_from_dicom.nii.gz found under {raw_dir}") |
| ensure_dir(cfg["paths"]["proc_dir"]) |
| items = list(cases.items()) |
| if not args.force: |
| items = [(c, p) for c, p in items |
| if not os.path.exists(os.path.join(cfg["paths"]["proc_dir"], f"{c}.npz"))] |
| print(f"[preprocess_cbct] {len(items)} case(s) to process (image-only, no GT).") |
| for cid, p in tqdm(items, desc="preprocess_cbct"): |
| try: |
| process_image_only(cid, p, cfg) |
| except Exception as e: |
| print(f"[preprocess_cbct] FAILED {cid}: {e}") |
| print(f"[preprocess_cbct] image-only npz -> {cfg['paths']['proc_dir']}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
