added utility function to get list of children regions

Author: guillaumelegoc

cuisto/utils.py

@@ -131,14 +131,7 @@ def get_blacklist(file: str, atlas: BrainGlobeAtlas) -> list:
 
     # add regions and their descendants
     for region in content["WITH_CHILDS"]["members"]:
-        blacklist.extend(
-            [
-                atlas.structures[id]["acronym"]
-                for id in atlas.structures.tree.expand_tree(
-                    atlas.structures[region]["id"]
-                )
-            ]
-        )
+        blacklist.extend(get_child_regions(atlas, region))
 
     # add regions specified exactly (no descendants)
     blacklist.extend(content["EXACT"]["members"])
@@ -198,6 +191,29 @@ def get_leaves_list(atlas: BrainGlobeAtlas) -> list:
     return leaves_list
 
 
+def get_child_regions(atlas: BrainGlobeAtlas, parent_region: str) -> list:
+    """
+    Get list of regions that are child of `parent_region`.
+
+    Parameters
+    ----------
+    atlas : BrainGlobeAtlas
+        Atlas to extract regions from.
+
+    Returns
+    -------
+    child_list : list
+        List of regions.
+
+    """
+    return [
+        atlas.structures[id]["acronym"]
+        for id in atlas.structures.tree.expand_tree(
+            atlas.structures[parent_region]["id"]
+        )
+    ]
+
+
 def ccf_to_stereo(
     x_ccf: float | np.ndarray, y_ccf: float | np.ndarray, z_ccf: float | np.ndarray = 0
 ) -> tuple:

docs/demo_notebooks/cells_distributions.ipynb

@@ -912,7 +912,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "hq",
+   "display_name": "cuisto-env",
    "language": "python",
    "name": "python3"
   },
@@ -926,7 +926,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cuisto"
-version = "2024.12.19.1"
+version = "2025.01.07"
 authors = [{ name = "Guillaume Le Goc", email = "g.legoc@posteo.org" }]
 description = "Quantification of objects in histological slices"
 readme = "README.md"