code/whole_case_compare_patch_v2/README.md

# CBCT Whole-Case Compare V2

This version fixes the overlap bug by baking every method-column translation
directly into mesh vertices with `mesh.apply_translation(...)`.

Final layout in ONE GLB:

LEFT -> RIGHT

1. Ground Truth
2. GeoCanal-SDF (Ours)
3. U-Mamba2
4. nnU-Net ResEnc L
5. MedNeXt-M k5

## Install

```bash
cd /root/autodl-tmp
rm -rf CBCT_whole_case_compare_patch_v2
unzip -q CBCT_whole_case_compare_patch_v2.zip -d /root/autodl-tmp

bash /root/autodl-tmp/CBCT_whole_case_compare_patch_v2/install_to_cbct.sh
```

## First test: Case033

```bash
cd /root/autodl-tmp/cbct
source /root/autodl-tmp/toothcanal_private/envs/core/bin/activate

rm -rf /root/autodl-tmp/toothcanal_private/clinical_whole_compare_v2/C033

python -m clinical_compare.whole_case_compare \
  --config benchmark_configs/private29_4fold_final.yaml \
  --cases 33 \
  --methods gt dualsdf_v21 umamba2 nnunet_resenc mednext \
  --gap-mm 35 \
  --preview \
  --strict \
  --out-dir /root/autodl-tmp/toothcanal_private/clinical_whole_compare_v2
```

Expected:

```text
C033/
  C033_GT_Ours_SOTA_5dentitions.glb
  C033_GT_Ours_SOTA_5dentitions_canals_only.glb
  C033_preview_5dentitions.png
  layout.csv
  READ_ME_FIRST.txt
```

The terminal prints five separate X intervals. They must NOT overlap.

## Final held-out cases

```bash
python -m clinical_compare.whole_case_compare \
  --config benchmark_configs/private29_4fold_final.yaml \
  --cases 31 32 33 34 35 \
  --methods gt dualsdf_v21 umamba2 nnunet_resenc mednext \
  --gap-mm 35 \
  --preview \
  --strict \
  --out-dir /root/autodl-tmp/toothcanal_private/clinical_whole_compare_v2
```

## Spacing

Recommended:
`--gap-mm 35`

If visually crowded:
`--gap-mm 50`

If too far:
`--gap-mm 25`

The gap is edge-to-edge empty space between complete dentitions.