Fixing princeton_mouse atlas mesh (#253)

* removing rotated_annotations to fix mesh orientation * set mesh scaling to True * remove unnecessary line was commented out and a relic of former brainrender issues --------- Co-authored-by: Alessandro Felder <[email protected]>
brainglobe · Mar 11, 2024 · f1371df · f1371df
1 parent e5296d7
commit f1371df
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py
@@ -127,9 +127,8 @@ def add_parent_id(child_id):
     meshes_dir_path.mkdir(exist_ok=True)
 
     tree = get_structures_tree(structs_dict)
-    rotated_annotations = np.rot90(annotated_volume, axes=(0, 2))
 
-    labels = np.unique(rotated_annotations).astype(np.int32)
+    labels = np.unique(annotated_volume).astype(np.int32)
     for key, node in tree.nodes.items():
         if key in labels:
             is_label = True
@@ -153,7 +152,7 @@ def add_parent_id(child_id):
                         node,
                         tree,
                         labels,
-                        rotated_annotations,
+                        annotated_volume,
                         ROOT_ID,
                         closing_n_iters,
                         decimate_fraction,
@@ -177,7 +176,7 @@ def add_parent_id(child_id):
                     node,
                     tree,
                     labels,
-                    rotated_annotations,
+                    annotated_volume,
                     ROOT_ID,
                     closing_n_iters,
                     decimate_fraction,
@@ -232,6 +231,7 @@ def add_parent_id(child_id):
         hemispheres_stack=None,
         cleanup_files=False,
         compress=True,
+        scale_meshes=True,
     )
 
     return output_filename