Raise when invalid space spec is supplied to get_map. Fixes #453

FZJ-INM1-BDA · Oct 24, 2023 · 72578ac · 72578ac
1 parent 8161f73
commit 72578ac
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Showing 3 changed files with 28 additions and 17 deletions.
diff --git a/siibra/core/parcellation.py b/siibra/core/parcellation.py
@@ -137,7 +137,12 @@ def matches(self, spec):
                 return True
         return super().matches(spec)
 
-    def get_map(self, space=None, maptype: Union[str, MapType] = MapType.LABELLED, spec: str = ""):
+    def get_map(
+        self,
+        space=None,
+        maptype: Union[str, MapType] = MapType.LABELLED,
+        spec: str = ""
+    ):
         """
         Get the maps for the parcellation in the requested template space.
 
@@ -169,15 +174,17 @@ def get_map(self, space=None, maptype: Union[str, MapType] = MapType.LABELLED, s
         if not isinstance(maptype, MapType):
             maptype = MapType[maptype.upper()]
 
+        space_inst = parcellationmap._space.Space.registry()[space]
+
         candidates = [
             m for m in parcellationmap.Map.registry()
-            if m.space.matches(space)
+            if m.space.matches(space_inst)
             and m.maptype == maptype
             and m.parcellation
             and m.parcellation.matches(self)
         ]
         if len(candidates) == 0:
-            logger.error(f"No {maptype} map in {space} available for {str(self)}")
+            logger.error(f"No {maptype} map in '{space}' available for {str(self)}")
             return None
         if len(candidates) > 1:
             spec_candidates = [

diff --git a/siibra/volumes/parcellationmap.py b/siibra/volumes/parcellationmap.py
@@ -28,7 +28,7 @@
     Species,
     CompareMapsResult
 )
-from ..core import concept, space, parcellation, region as _region
+from ..core import concept, space as _space, parcellation, region as _region
 from ..locations import point, pointset
 from ..retrieval import requests
 
@@ -45,22 +45,26 @@
     from ..core.region import Region
 
 
-class ExcessiveArgumentException(ValueError): pass
+class ExcessiveArgumentException(ValueError):
+    pass
 
 
-class InsufficientArgumentException(ValueError): pass
+class InsufficientArgumentException(ValueError):
+    pass
 
 
-class ConflictingArgumentException(ValueError): pass
+class ConflictingArgumentException(ValueError):
+    pass
 
 
-class NonUniqueIndexError(RuntimeError): pass
+class NonUniqueIndexError(RuntimeError):
+    pass
 
 
 @dataclass
 class Assignment:
     input_structure: int
-    centroid: Union[Tuple[np.ndarray], point.Point] 
+    centroid: Union[Tuple[np.ndarray], point.Point]
     volume: int
     fragment: str
     map_value: np.ndarray
@@ -286,8 +290,8 @@ def get_region(self, label: int = None, volume: int = 0, index: MapIndex = None)
     def space(self):
         for key in ["@id", "name"]:
             if key in self._space_spec:
-                return space.Space.get_instance(self._space_spec[key])
-        return space.Space(None, "Unspecified space", species=Species.UNSPECIFIED_SPECIES)
+                return _space.Space.get_instance(self._space_spec[key])
+        return _space.Space(None, "Unspecified space", species=Species.UNSPECIFIED_SPECIES)
 
     @property
     def parcellation(self):
@@ -794,7 +798,7 @@ def _assign(
         minsize_voxel=1,
         lower_threshold=0.0,
         **kwargs
-    ) -> List[Union[Assignment,AssignImageResult]]:
+    ) -> List[Union[Assignment, AssignImageResult]]:
         """
         For internal use only. Returns a dataclass, which provides better static type checking.
         """
@@ -805,7 +809,7 @@ def _assign(
             return self._assign_points(item, lower_threshold)
         if isinstance(item, Nifti1Image):
             return self._assign_image(item, minsize_voxel, lower_threshold, **kwargs)
-        
+
         raise RuntimeError(
             f"Items of type {item.__class__.__name__} cannot be used for region assignment."
         )
@@ -1078,7 +1082,7 @@ def progress(it, N: int = None, desc: str = "", min_elements=5):
             seqlen = N or len(it)
             return iter(it) if seqlen < min_elements \
                 else siibra_tqdm(it, desc=desc, total=N)
-        
+
         iter_func = iterate_connected_components if split_components \
             else lambda img: [(1, img)]
 

diff --git a/test/volumes/test_parcellationmap.py b/test/volumes/test_parcellationmap.py
@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import patch, MagicMock
-from siibra.volumes.parcellationmap import Map, space, parcellation, MapType, MapIndex, ExcessiveArgumentException, InsufficientArgumentException, ConflictingArgumentException, NonUniqueIndexError
+from siibra.volumes.parcellationmap import Map, _space, parcellation, MapType, MapIndex, ExcessiveArgumentException, InsufficientArgumentException, ConflictingArgumentException, NonUniqueIndexError
 from siibra.commons import Species
 from siibra.core.region import Region
 from uuid import uuid4
@@ -95,8 +95,8 @@ def test_space(self, set_space_spec, called_arg, called_get_instance, return_spa
 
         self.map = TestMap.get_instance(space_spec=set_space_spec)
 
-        with patch.object(space.Space, 'get_instance') as mock_get_instance:
-            return_space = space.Space(None, "Returned Space", species=Species.HOMO_SAPIENS) if return_space_flag else None
+        with patch.object(_space.Space, 'get_instance') as mock_get_instance:
+            return_space = _space.Space(None, "Returned Space", species=Species.HOMO_SAPIENS) if return_space_flag else None
             mock_get_instance.return_value = return_space
 
             actual_returned_space = self.map.space