Make voi validity and cliping at Volume.fetch stage

FZJ-INM1-BDA · Oct 15, 2024 · 28e59b8 · 28e59b8
1 parent 28f6efb
commit 28e59b8
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Showing 3 changed files with 16 additions and 36 deletions.
diff --git a/siibra/volumes/providers/neuroglancer.py b/siibra/volumes/providers/neuroglancer.py
@@ -503,24 +503,7 @@ def fetch(self, voi: _boundingbox.BoundingBox = None, **kwargs):
         if voi is None:
             bbox_ = _boundingbox.BoundingBox((0, 0, 0), self.size, space=None)
         else:
-            if voi.space is not None:
-                # ensure the voi is inside the template
-                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:
-                    bbox_ = voi.transform(np.linalg.inv(self.affine))
-                else:
-                    logger.warning(
-                        (
-                            f"{voi=} provided was cliped to be in the voxel space of the {voi.space.name} template.\n",
-                            f"Clipped boundingbox={intersection_bbox}"
-                        )
-                    )
-                    bbox_ = intersection_bbox.transform(np.linalg.inv(self.affine))
-            else:
-                bbox_ = voi.transform(np.linalg.inv(self.affine))
+            bbox_ = voi.transform(np.linalg.inv(self.affine))
 
         for dim in range(3):
             if bbox_.shape[dim] < 1:

diff --git a/siibra/volumes/providers/nifti.py b/siibra/volumes/providers/nifti.py
@@ -188,24 +188,7 @@ def fetch(
             result = loader()
 
         if voi is not None:
-            if voi.space is not None:
-                # ensure the voi is inside the template
-                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:
-                    bb_vox = voi.transform(np.linalg.inv(result.affine))
-                else:
-                    logger.warning(
-                        (
-                            f"{voi=} provided was cliped to be in the voxel space of the {voi.space.name} template.\n",
-                            f"Clipped boundingbox={intersection_bbox}"
-                        )
-                    )
-                    bb_vox = intersection_bbox.transform(np.linalg.inv(result.affine))
-            else:
-                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

diff --git a/siibra/volumes/volume.py b/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: