maint fig5 notebook

Author: AhmetNSimsek

examples/tutorials/2025-paper-fig5.py

@@ -46,8 +46,7 @@
 # First we retrieve the probability map of a motor area
 # from the Julich-Brain cytoarchitectonic atlas.
 region = siibra.get_region("julich 3.0.3", "4p right")
-probmaps = region.parcellation.get_map("mni152", "statistical")
-region_map = probmaps.get_volume(region)
+region_map = region.get_regional_map("mni152", "statistical")
 
 # %%
 # We can use the probability map as a query to extract 1 micron resolution
@@ -84,10 +83,7 @@
 # Next we plot the section itself and identify the larger region of
 # interest around the patch, using the bounding box
 # of the centers of most relevant patches with a bit of padding.
-patch_locations = siibra.PointCloud(
-    [tuple(p.get_boundingbox().center) for p in patches],
-    space='bigbrain'
-)
+patch_locations = siibra.PointCloud.union(*[p.get_boundingbox().center for p in patches])
 roi = patch_locations.boundingbox.zoom(1.5)
 
 # fetch the section at reduced resolution for plotting.
@@ -139,7 +135,7 @@
 # %%
 # Plot the region of interest again, this time with the cortical profile that
 # defined the patch, as well as other candidate patch's locations
-# with their relevance scores, ie. probabilities. 
+# with their relevance scores, ie. probabilities.
 display = plotting.plot_img(roi_img, display_mode="y", cmap='gray', annotate=False)
 ax = list(display.axes.values())[0].ax
 
@@ -156,5 +152,3 @@
 ax.plot(X, Z, "r-", lw=2)
 
 # sphinx_gallery_thumbnail_number = -2
-
-# %%

siibra/features/image/sections.py

@@ -83,9 +83,9 @@ def __repr__(self):
     def section(self) -> CellbodyStainedSection:
         return self._section
 
-    def get_boundingbox(self):
-        """ Enforce that the bounding box spans the full section thickness."""
-        bbox_section = self._section.get_boundingbox()
+    def get_boundingbox(self, **fetch_kwargs):
+        """Enforce that the bounding box spans the full section thickness."""
+        bbox_section = self._section.get_boundingbox(**fetch_kwargs)
         bbox = self._patch.boundingbox
         bbox.minpoint[1] = bbox_section.minpoint[1]
         bbox.maxpoint[1] = bbox_section.maxpoint[1]