Create anchors of BigBrainIntensity features in bigbrain.py to use th…

…e same logic and avoid unnecessary imports
FZJ-INM1-BDA · Dec 14, 2023 · 4d6f42f · 4d6f42f
1 parent 09c8830
commit 4d6f42f
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Showing 3 changed files with 21 additions and 22 deletions.
diff --git a/siibra/features/tabular/bigbrain_intensity_profile.py b/siibra/features/tabular/bigbrain_intensity_profile.py
@@ -17,7 +17,7 @@
 
 from typing import List, TYPE_CHECKING
 if TYPE_CHECKING:
-    from ...locations import point
+    from ...features.anchor import AnatomicalAnchor
 
 
 class BigBrainIntensityProfile(
@@ -40,18 +40,11 @@ class BigBrainIntensityProfile(
 
     def __init__(
         self,
-        regionname: str,
+        anchor: "AnatomicalAnchor",
         depths: list,
         values: list,
-        boundaries: list,
-        location: 'point.Point'
+        boundaries: list
     ):
-        from ..anchor import AnatomicalAnchor
-        anchor = AnatomicalAnchor(
-            location=location,
-            region=regionname,
-            species='Homo sapiens'
-        )
         cortical_profile.CorticalProfile.__init__(
             self,
             description=self.DESCRIPTION,

diff --git a/siibra/features/tabular/layerwise_bigbrain_intensities.py b/siibra/features/tabular/layerwise_bigbrain_intensities.py
@@ -19,6 +19,10 @@
 import pandas as pd
 import numpy as np
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from ...features.anchor import AnatomicalAnchor
+
 
 class LayerwiseBigBrainIntensities(
     tabular.Tabular,
@@ -39,16 +43,10 @@ class LayerwiseBigBrainIntensities(
 
     def __init__(
         self,
-        regionname: str,
+        anchor: "AnatomicalAnchor",
         means: list,
         stds: list,
     ):
-
-        from ..anchor import AnatomicalAnchor
-        anchor = AnatomicalAnchor(
-            region=regionname,
-            species='Homo sapiens',
-        )
         data = pd.DataFrame(
             np.array([means, stds]).T,
             columns=['mean', 'std'],

diff --git a/siibra/livequeries/bigbrain.py b/siibra/livequeries/bigbrain.py
@@ -88,12 +88,16 @@ def query(self, concept: structure.BrainStructure, **kwargs) -> List[bigbrain_in
         matched = concept.intersection(pointset.PointSet(loader._vertices, space='bigbrain'))
         assert matched.labels is not None
         for i in matched.labels:
+            anchor = _anchor.AnatomicalAnchor(
+                location=point.Point(loader._vertices[i], space='bigbrain'),
+                region=str(concept),
+                species='Homo sapiens'
+            )
             prof = bigbrain_intensity_profile.BigBrainIntensityProfile(
-                regionname=str(concept),
+                anchor=anchor,
                 depths=loader.profile_labels,
                 values=loader._profiles[i],
-                boundaries=loader._boundary_depths[i],
-                location=point.Point(loader._vertices[i], space='bigbrain')
+                boundaries=loader._boundary_depths[i]
             )
             prof.anchor._assignments[concept] = _anchor.AnatomicalAssignment(
                 query_structure=concept,
@@ -128,12 +132,16 @@ def query(self, concept: structure.BrainStructure, **kwargs) -> List[layerwise_b
             for b in boundary_depths
         ]).reshape((-1, 200))
 
+        anchor = _anchor.AnatomicalAnchor(
+            location=pointset.PointSet(loader._vertices[indices, :], space='bigbrain'),
+            region=str(concept),
+            species='Homo sapiens'
+        )
         result = layerwise_bigbrain_intensities.LayerwiseBigBrainIntensities(
-            regionname=str(concept),
+            anchor=anchor,
             means=[matched_profiles[layer_labels == layer].mean() for layer in range(1, 7)],
             stds=[matched_profiles[layer_labels == layer].std() for layer in range(1, 7)],
         )
-        result.anchor._location_cached = pointset.PointSet(loader._vertices[indices, :], space='bigbrain')
         result.anchor._assignments[concept] = _anchor.AnatomicalAssignment(
             query_structure=concept,
             assigned_structure=concept,