provider.boundingbox -> provider.get_boundingbox()

Solves bounding box of region's possibly resulting to be the whole space

Author: AhmetNSimsek

e2e/core/test_region.py

@@ -106,3 +106,20 @@ def test_related_region_hemisphere():
     all_related_reg = [reg for reg in reg.get_related_regions()]
     assert any("left" in ass.assigned_structure.name for ass in all_related_reg)
     assert any("right" in ass.assigned_structure.name for ass in all_related_reg)
+
+
+spaces = ['mni152', 'colin27']
+
+
+@pytest.mark.parametrize("space", spaces)
+def test_boundingbox(space):
+    hoc1_l = siibra.get_region('julich', 'hoc1 left')
+    hoc1_r = siibra.get_region('julich', 'hoc1 right')
+    bbox_l = hoc1_l.get_bounding_box(space)
+    bbox_r = hoc1_r.get_bounding_box(space)
+    assert bbox_l != bbox_r, "Left and right hoc1 should not have the same bounding boxes"
+
+    v_l = hoc1_l.get_regional_map(space)
+    v_r = hoc1_r.get_regional_map(space)
+    assert bbox_l == v_l.boundingbox, "Boundingbox of regional mask should be the same as bouding mask of the regions"
+    assert bbox_r == v_r.boundingbox, "Boundingbox of regional mask should be the same as bouding mask of the regions"

siibra/core/region.py

@@ -17,7 +17,7 @@
 from . import concept, structure, space as _space, parcellation as _parcellation
 from .assignment import Qualification, AnatomicalAssignment
 
-from ..locations import location, boundingbox, point, pointset
+from ..locations import location, point, pointset
 from ..volumes import parcellationmap, volume
 from ..commons import (
     logger,

siibra/volumes/providers/gifti.py

@@ -44,8 +44,7 @@ def __init__(self, url: Union[str, Dict[str, str]], volume=None):
     def _url(self) -> Union[str, Dict[str, str]]:
         return self._init_url
 
-    @property
-    def boundingbox(self) -> _boundingbox.BoundingBox:
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
         raise NotImplementedError(
             f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
         )
@@ -143,10 +142,9 @@ def fetch(self, fragment: str = None, **kwargs):
 
         return {"labels": np.hstack(labels)}
 
-    @property
-    def boundingbox(self) -> _boundingbox.BoundingBox:
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
         raise NotImplementedError(
-            f"Bounding boxes of {self.__class__.__name__} objects not defined."
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
         )
 
     @property

siibra/volumes/providers/neuroglancer.py

@@ -118,22 +118,35 @@ def fetch(
 
         return result
 
-    @property
-    def boundingbox(self):
+    def get_boundingbox(self, clip=False, background=0) -> "_boundingbox.BoundingBox":
         """
         Return the bounding box in physical coordinates
         of the union of fragments in this neuroglancer volume.
         """
         bbox = None
         for frag in self._fragments.values():
-            next_bbox = _boundingbox.BoundingBox((0, 0, 0), frag.shape, space=None) \
-                .transform(frag.affine)
+            if len(frag.shape) > 3:
+                logger.warning(
+                    f"N-D Neuroglancer volume has shape {frag.shape}, but "
+                    f"bounding box considers only {frag.shape[:3]}"
+                )
+            if clip:
+                img = frag.fetch()
+                bounds = _boundingbox.BoundingBox._determine_bounds(np.asanyarray(img.dataobj), background)
+                next_bbox = _boundingbox.BoundingBox(
+                    bounds[:3, 0], bounds[:3, 1], space=None
+                )
+            else:
+                shape = frag.shape[:3]
+                next_bbox = _boundingbox.BoundingBox(
+                    (0, 0, 0), shape, space=None
+                ).transform(frag.affine)
             bbox = next_bbox if bbox is None else bbox.union(next_bbox)
         return bbox
 
     def _merge_fragments(self) -> nib.Nifti1Image:
         # TODO this only performs nearest neighbor interpolation, optimized for float types.
-        bbox = self.boundingbox
+        bbox = self.get_boundingbox(clip=False, background=0.0)
         num_conflicts = 0
         result = None
 
@@ -486,10 +499,9 @@ def __init__(self, resource: Union[str, dict], volume=None):
     def _url(self) -> Union[str, Dict[str, str]]:
         return self._init_url
 
-    @property
-    def boundingbox(self) -> _boundingbox.BoundingBox:
+    def get_boundingbox(self, clip=False, background=0.0) -> '_boundingbox.BoundingBox':
         raise NotImplementedError(
-            f"Fast bounding box access to {self.__class__.__name__} objects not yet implemented."
+            f"Bounding box access to {self.__class__.__name__} objects not yet implemented."
         )
 
     def _get_fragment_info(self, meshindex: int) -> Dict[str, Tuple[str, ]]:

siibra/volumes/providers/nifti.py

@@ -65,8 +65,7 @@ def _url(self) -> Union[str, Dict[str, str]]:
     def fragments(self):
         return [k for k in self._img_loaders if k is not None]
 
-    @property
-    def boundingbox(self):
+    def get_boundingbox(self, clip=True, background=0) -> "_boundingbox.BoundingBox":
         """
         Return the bounding box in physical coordinates
         of the union of fragments in this nifti volume.
@@ -79,15 +78,22 @@ def boundingbox(self):
                     f"N-D NIfTI volume has shape {img.shape}, but "
                     f"bounding box considers only {img.shape[:3]}"
                 )
-            shape = img.shape[:3]
-            next_bbox = _boundingbox.BoundingBox((0, 0, 0), shape, space=None) \
-                .transform(img.affine)
+            if clip:
+                bounds = _boundingbox.BoundingBox._determine_bounds(np.asanyarray(img.dataobj), background)
+                next_bbox = _boundingbox.BoundingBox(
+                    bounds[:3, 0], bounds[:3, 1], space=None
+                )
+            else:
+                shape = img.shape[:3]
+                next_bbox = _boundingbox.BoundingBox(
+                    (0, 0, 0), shape, space=None
+                ).transform(img.affine)
             bbox = next_bbox if bbox is None else bbox.union(next_bbox)
         return bbox
 
     def _merge_fragments(self) -> nib.Nifti1Image:
         # TODO this only performs nearest neighbor interpolation, optimized for float types.
-        bbox = self.boundingbox
+        bbox = self.get_boundingbox(clip=True, background=0.0)
         num_conflicts = 0
         result = None
 

siibra/volumes/providers/provider.py

@@ -35,9 +35,8 @@ def __init_subclass__(cls, srctype: str) -> None:
         VolumeProvider._SUBCLASSES.append(cls)
         return super().__init_subclass__()
 
-    @property
     @abstractmethod
-    def boundingbox(self) -> "BoundingBox":
+    def get_boundingbox(self, clip=True, background=0.0) -> "BoundingBox":
         raise NotImplementedError
 
     @property
@@ -84,9 +83,8 @@ def __init__(self, parent_provider: VolumeProvider, z: int):
         self.srctype = parent_provider.srctype
         self.z = z
 
-    @property
-    def boundingbox(self) -> "BoundingBox":
-        return self.provider.boundingbox
+    def get_boundingbox(self, clip=True, background=0.0) -> "BoundingBox":
+        return self.provider.get_boundingbox(clip=clip, background=background)
 
     def fetch(self, **kwargs):
         # activate caching at the caller using "with SubvolumeProvider.UseCaching():""

siibra/volumes/volume.py

@@ -119,7 +119,7 @@ def concat(url: Union[str, Dict[str, str]], concat: str):
     def boundingbox(self):
         for provider in self._providers.values():
             try:
-                bbox = provider.boundingbox
+                bbox = provider.get_boundingbox()
                 if bbox.space is None:  # provider does usually not know the space!
                     bbox._space_cached = self.space
                     bbox.minpoint._space_cached = self.space

test/volumes/test_volume.py

@@ -15,8 +15,7 @@ def fetch(self, *args, **kwargs):
     def _url(self):
         return {}
 
-    @property
-    def boundingbox(self):
+    def get_boundingbox(self, clip=True, background=0):
         return None