chore: require TPTBox ^1.0.0

pyproject.toml

@@ -26,15 +26,17 @@ pytorch-lightning = "^2.0.8"
 torchmetrics = "^1.1.2"
 tqdm = "^4.66.1"
 einops= "^0.6.1"
-TPTBox = "^0.8.1"
+TPTBox = "^1.0.0"
 # TPTBox needs ants.utils.nibabel_nifti_to_ants, which only exists from antspyx 0.6 on, and antspyx ships no
 # Windows/macOS cp39 wheel from 0.6.0 on -- so Python 3.9 is Linux-only (see the CI matrix exclude).
 antspyx = "0.6.3"
 rich = "^13.6.0"
 monai="^1.3.0"
 TypeSaveArgParse="^1.0.1"
-# nnunetv2/acvl-utils/blosc2/python-gdcm are transitive dependencies of TPTBox's nnU-Net inference path
-# (TPTBox.segmentation.nnUnet_utils.inference_api); pinned directly here to control the resolved versions.
+# nnunetv2/acvl-utils/blosc2/python-gdcm back TPTBox's nnU-Net inference path
+# (TPTBox.segmentation.nnUnet_utils.inference_api). TPTBox 1.0 moved them into its optional `seg`
+# extra, so they are required here rather than pulled in transitively; pinned directly to control
+# the resolved versions. torch comes in via pytorch-lightning, batchgenerators via nnunetv2.
 python-gdcm = [
   { version = "==3.0.25", python = ">=3.9,<3.10" },
 ]

spineps/phase_post.py

@@ -750,12 +750,16 @@ def detect_and_solve_merged_vertebra(seg_nii: NII, vert_nii: NII) -> tuple[NII,
         # both vertebra
         if first_stats[2] < MERGED_VERTEBRA_SIZE_RATIO * second_stats[2]:
             # first is significantly smaller than second and they are close in height
-            # how many pixels are touching
-            vert_firsttwo_arr = vert_nii.extract_label(first_key).get_seg_array()
-            vert_firsttwo_arr2 = vert_nii.extract_label(second_key).get_seg_array()
-            vert_firsttwo_arr += vert_firsttwo_arr2 + 1
+            # Paint the two instances as 1 and 2 with the background left at 0, so the contact count
+            # is the one between the two vertebrae. Adding the two binary masks plus one instead
+            # labelled the background 1 and *both* vertebrae 2, so `(1, 2)` measured the outer
+            # surface of the pair and the branch fired on virtually any pair of top instances.
+            # `extract_label` also returns a boolean mask, which cannot be accumulated into in place.
+            vert_firsttwo_arr = vert_nii.extract_label(first_key).get_seg_array().astype(np.uint8)
+            vert_firsttwo_arr[vert_nii.extract_label(second_key).get_seg_array() != 0] = 2
             contacts = np_contacts(vert_firsttwo_arr, connectivity=3)
-            if contacts[(1, 2)] > isotropic_area_to_voxels(MERGED_VERTEBRA_MIN_CONTACT_MM2, vert_nii.zoom):
+            # cc3d only reports label pairs that actually touch.
+            if contacts.get((1, 2), 0) > isotropic_area_to_voxels(MERGED_VERTEBRA_MIN_CONTACT_MM2, vert_nii.zoom):
                 logger.print("Found first two instance weird, will merge", Log_Type.STRANGE)
                 vert_nii.map_labels_({first_key: second_key}, verbose=False)
 

unit_tests/test_bugfixes.py

@@ -64,12 +64,35 @@ def _fixture() -> tuple[NII, NII]:
         seg[3:9, 37:39, 3:9] = 100  # an IVD below them, so the disc branch has something to find
         return _nii(seg), _nii(vert)
 
+    @staticmethod
+    def _detached_fixture() -> tuple[NII, NII]:
+        """Same shape as ``_fixture``, but with a gap between the two top instances.
+
+        They never touch, so the split-C2 heuristic must leave them alone. The old encoding
+        (background 1, both vertebrae 2) measured the outer surface of the pair instead of their
+        mutual contact, so this case was merged too.
+        """
+        shape = (12, 40, 12)
+        seg = np.zeros(shape, dtype=np.uint8)
+        vert = np.zeros(shape, dtype=np.uint8)
+        seg[3:9, 20:23, 3:9] = 49  # small instance 1
+        vert[3:9, 20:23, 3:9] = 1
+        seg[3:9, 27:37, 3:9] = 49  # large instance 2, four voxels below it
+        vert[3:9, 27:37, 3:9] = 2
+        seg[3:9, 37:39, 3:9] = 100  # an IVD below them
+        return _nii(seg), _nii(vert)
+
     def test_top_two_instances_are_merged(self):
         seg_nii, vert_nii = self._fixture()
         detect_and_solve_merged_vertebra(seg_nii, vert_nii)
         self.assertNotIn(1, vert_nii.unique(), "the small top instance should have been merged into its neighbour")
         self.assertIn(2, vert_nii.unique())
 
+    def test_detached_top_instance_is_kept(self):
+        seg_nii, vert_nii = self._detached_fixture()
+        detect_and_solve_merged_vertebra(seg_nii, vert_nii)
+        self.assertEqual([1, 2], list(vert_nii.unique()), "instances that do not touch must not be merged")
+
 
 class Test_Semantic_Bounding_Box_Clean(unittest.TestCase):
     """The region kept must be the union of the incorporated components' boxes, not just the largest."""