Merge pull request #200 from FZJ-INM1-BDA/bugfix_multipleCentorids

WIP fix when multiple centroids are available

Author: xgui3783

siibra/__init__.py

@@ -16,7 +16,7 @@
 from .commons import logger, QUIET, VERBOSE
 
 # __version__ is parsed by setup.py
-__version__ = "0.3a22"
+__version__ = "0.3a23"
 logger.info(f"Version: {__version__}")
 logger.warning("This is a development release. Use at your own risk.")
 logger.info(

siibra/core/region.py

@@ -971,7 +971,9 @@ def vol_to_id_dict(vol: VolumeSrc):
             if detail:
                 try:
                     centroids = self.centroids(space)
-                    assert len(centroids) == 1, f"expect a single centroid as return for centroid(space) call, but got {len(centroids)} results."
+                    assert len(centroids) > 0, f"Region.to_model detailed flag set, expect a single centroid as return for centroid(space) call, but got none."
+                    if len(centroids) != 1:
+                        logger.warn(f"Region.to_model detailed flag set. Can only handle one and only one centroid, but got {len(centroids)}. Using the first one, if available, or return None")
                     pev.has_annotation.best_view_point = BestViewPoint(
                         coordinate_space={
                             "@id": space.model_id
@@ -983,6 +985,9 @@ def vol_to_id_dict(vol: VolumeSrc):
                             }
                         ) for pt in centroids[0]]
                     )
+                except AssertionError as e:
+                    # no centroids found. Log warning, but do not raise.
+                    logger.warn(e)
                 except NotImplementedError:
                     # Region masks for surface spaces are not yet supported. for surface-based spaces
                     pass

test/core/test_region.py

@@ -140,6 +140,20 @@ def test_region_to_model(region: Region):
     # import re
     # assert re.match(r"^[\w/\-.:]+$", model.id), f"model_id should only contain [\w/\-.:]+, but is instead {model.id}"
 
+
+detailed_region_in_space = [
+    ("minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe-v4", "stria medullaris thalami", "minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8")
+]
+@pytest.mark.parametrize('parc_id,region_id,space_id', detailed_region_in_space)
+def test_detailed_region_in_space(parc_id,region_id,space_id):
+    p = siibra.parcellations[parc_id]
+    assert p is not None
+    r = p.decode_region(region_id)
+    assert r is not None
+    s = siibra.spaces[space_id]
+    assert s is not None
+    r.to_model(detail=True, space=s)
+
 detailed_region=[
     ("julich 2.9", "hoc1 left", "mni152", False, True),
     ("julich 2.9", "hoc1 right", "mni152", False, True),