File size: 2,605 Bytes
c4c5273 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | """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()
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