clip voi to template's to if voi lies partially outside of the template

e2e/volumes/test_extracting_bbox_from_template.py

@@ -0,0 +1,23 @@
+import pytest
+import siibra
+from nibabel import Nifti1Image
+
+
+vois = [
+    siibra.locations.BoundingBox(
+        (-54.90, -29.47, 12.66), (12.69, 35.12, 20.24), "bigbrain"
+    ),
+    siibra.locations.BoundingBox(
+        (-154.90, -29.47, 12.66), (112.69, 38.12, 80.24), "bigbrain"
+    ),
+    siibra.locations.BoundingBox(
+        (-54.90, -29.47, 12.66), (12.69, 38.12, 80.24), "bigbrain"
+    ),
+]
+
+
+@pytest.mark.parametrize("voi", vois)
+def test_fetching_voi(voi):
+    assert isinstance(
+        voi.space.get_template().fetch(voi=voi, resolution_mm=0.52), Nifti1Image
+    )

siibra/volumes/providers/nifti.py

@@ -188,7 +188,7 @@ def fetch(
             result = loader()
 
         if voi is not None:
-            bb_vox = voi.transform(np.linalg.inv(result.affine))
+            bb_vox = voi.transform(np.linalg.inv(self.affine))
             (x0, y0, z0), (x1, y1, z1) = bb_vox.minpoint, bb_vox.maxpoint
             shift = np.identity(4)
             shift[:3, -1] = bb_vox.minpoint

siibra/volumes/volume.py

@@ -416,6 +416,20 @@ def fetch(
                 f"volume are: {self.formats}"
             )
 
+        # ensure the voi is inside the template
+        voi = kwargs.get("voi", None)
+        if voi is not None and voi.space is not None:
+            assert isinstance(voi, boundingbox.BoundingBox)
+            tmplt_bbox = voi.space.get_template().get_boundingbox(clip=False)
+            intersection_bbox = voi.intersection(tmplt_bbox)
+            if intersection_bbox is None:
+                raise RuntimeError(f"{voi=} provided lies out side the voxel space of the {voi.space.name} template.")
+            if intersection_bbox != voi:
+                logger.info(
+                    f"Since provided voi lies outside the template ({voi.space}) it is clipped as: {intersection_bbox}"
+                )
+                kwargs["voi"] = intersection_bbox
+
         result = None
         # try each possible format
         for fmt in possible_formats: