Fix bug fetching gii-label map. Satisfy Flake8. vertices_labels->`v…

…ertex_labels`

examples/02_maps_and_templates/005_access_surface_maps.py

@@ -52,13 +52,12 @@
 # first one from the list. Now let us fetch a specific variant and also the
 # hemisphere fragment
 mesh = mp.fetch(variant="inflated", fragment="left")
-
-# The returned structure is a dictionary of three numpy arrays representing the
-# vertices, faces, and labels respectively. Each vertex defines a 3D surface
+mesh
+# The returned structure is a Surface consiting of three numpy arrays representing the
+# vertices, faces, and vertex_labels respectively. Each vertex defines a 3D surface
 # point, while the faces are triplets of indices into the list of vertices,
 # defining surface triangles. The labels provide the label index associated with
 # each vertex.
-print(mesh.keys())
 
 # %%
 # Most meshes are shipped with a color map which we can fetch from the map

siibra/surface/common.py

@@ -4,32 +4,43 @@
 from io import BytesIO
 from functools import wraps
 
+
 class Surface:
-    def __init__(self, vertices: List[List[float]]=None,
-                 faces: List[List[int]]=None,
-                 vertices_labels: List[List[Union[float, int]]]=None,
-                 **kwargs) -> None:
-        """Describes a common interface to surface, where vertices
+    def __init__(
+        self,
+        vertices: List[List[float]] = None,
+        faces: List[List[int]] = None,
+        vertex_labels: List[List[Union[float, int]]] = None,
+        **kwargs,
+    ) -> None:
+        """
+        Describes a common interface to surface, where vertices
         faces are defined, and optionally, vertices labels, face labels
         can be defined.
-        
-        Args:
-            vertices (List[List[float]] or ndarray): verticies triplet
-            faces: (List[List[int]] or ndarray): faces triplet
-            vertices_labels: (Labels)"""
-
-        self.vertices = np.array(kwargs.get("verts", []) if vertices is None else vertices)
+
+        Parameters
+        ----------
+        vertices (List[List[float]] or ndarray): verticies triplet
+        faces: (List[List[int]] or ndarray): faces triplet
+        vertex_labels: (Labels)
+        """
+
+        self.vertices = np.array(
+            kwargs.get("verts", []) if vertices is None else vertices
+        )
         self.faces = np.array([] if faces is None else faces, dtype=np.uint64)
 
-        vertices_labels = kwargs.get("labels", []) if vertices_labels is None else vertices_labels
-        self.vertices_labels = np.array(vertices_labels)
+        vertex_labels = (
+            kwargs.get("labels", []) if vertex_labels is None else vertex_labels
+        )
+        self.vertex_labels = np.array(vertex_labels)
 
     def __contains__(self, spec):
         self.faces
         if spec in ("verts", "faces"):
             return True
         if spec == "labels":
-            return len(self.vertices_labels) > 0
+            return len(self.vertex_labels) > 0
         return False
 
     def __getitem__(self, spec: str):
@@ -38,10 +49,10 @@ def __getitem__(self, spec: str):
         if spec == "faces":
             return self.faces
         if spec == "labels":
-            if len(self.vertices_labels) > 0:
-                return self.vertices_labels
+            if len(self.vertex_labels) > 0:
+                return self.vertex_labels
         raise IndexError(f"spec {spec!r} not found in class surface")
-    
+
     def export(self, export_dest: Union[str, IO]):
         mesh = trimesh.Trimesh(self.vertices, self.faces)
         mesh.export(export_dest)
@@ -53,11 +64,14 @@ def to_bytes(self):
         io.seek(0)
         return io.read()
 
+
 def wrap_return_surface():
     def outer(fn):
         @wraps(fn)
         def inner(*args, **kwargs):
             return_val = fn(*args, **kwargs)
             return Surface(**return_val)
+
         return inner
+
     return outer

siibra/volumes/volume.py

@@ -346,9 +346,8 @@ def fetch(
                 try:
                     if fmt == "gii-label":
                         tpl = self.space.get_template(variant=kwargs.get('variant'))
-                        mesh = tpl.fetch(**kwargs)
-                        labels = self._providers[fmt].fetch(**fwd_args)
-                        result = dict(**mesh, **labels)
+                        result = tpl.fetch(format='mesh', **kwargs)
+                        result.vertex_labels = self._providers[fmt].fetch(**fwd_args).get('labels')
                     else:
                         result = self._providers[fmt].fetch(**fwd_args)
                 except requests.SiibraHttpRequestError as e: