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3799002 | 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 | """Export ground-truth meshes (tooth + canal) for the held-out test cases by
running marching cubes directly on the CLEANED label volume in WORLD coords.
This lets you compare GT vs prediction as two separate assembled scenes.
python -m toothcanal.export_gt --config configs/default.yaml
"""
import os, argparse
import numpy as np
from .utils import load_config, ensure_dir
from .splits import make_split
from .geometry import sdf_from_mask, marching_cubes_to_mesh
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--config", default="configs/default.yaml")
args = ap.parse_args()
cfg = load_config(args.config)
_, test = make_split(cfg["paths"]["proc_dir"], cfg)
out_dir = ensure_dir(os.path.join(cfg["paths"]["out_dir"], "gt_meshes"))
for cid in test:
d = dict(np.load(os.path.join(cfg["paths"]["proc_dir"], f"{cid}.npz")))
inst = d["inst"]; cinst = d["cinst"]
sp = d["spacing"].astype(np.float32)
origin = d.get("origin", np.zeros(3)).astype(np.float32)
ids = [int(v) for v in np.unique(inst) if v > 0]
print(f"[gt] {cid}: {len(ids)} teeth")
for iid in ids:
tooth_mask = (inst == iid)
canal_mask = (cinst == iid)
for name, mask in [("tooth", tooth_mask), ("canal", canal_mask)]:
if not mask.any():
continue
# crop to bbox + small pad to keep MC fast
ax = np.argwhere(mask)
lo = ax.min(0) - 2; hi = ax.max(0) + 3
lo = np.maximum(lo, 0); hi = np.minimum(hi, mask.shape)
sl = tuple(slice(int(a), int(b)) for a, b in zip(lo, hi))
sdf = sdf_from_mask(mask[sl], sp)
mesh = marching_cubes_to_mesh(sdf, 0.0, sp)
if mesh is None:
continue
# shift to world coords
mesh.vertices += (origin + lo * sp)[None, :]
mesh.export(os.path.join(out_dir, f"{cid}_t{iid:02d}_{name}_GT.stl"))
print(f"[gt] written GT meshes to {out_dir}")
if __name__ == "__main__":
main()
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