feat: allow meshes to be exported

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

requirements.txt

@@ -8,3 +8,4 @@ nilearn
 typing-extensions; python_version < "3.8"
 filelock
 ebrains-drive >= 0.6.0
+trimesh

setup.py

@@ -53,5 +53,6 @@ def find_version():
         'typing-extensions; python_version < "3.8"',
         "filelock",
         "ebrains-drive >= 0.6.0",
+        "trimesh",
     ],
 )

siibra/commons.py

@@ -14,6 +14,8 @@
 # limitations under the License.
 """Constants, functions, and classes used commonly across siibra."""
 
+from .surface import wrap_return_surface
+
 import os
 import re
 from enum import Enum
@@ -677,6 +679,7 @@ def is_mesh(structure: Union[list, dict]):
         return False
 
 
+@wrap_return_surface()
 def merge_meshes(meshes: list, labels: list = None):
     # merge a list of meshes into one
     # if meshes have no labels, a list of labels of the

siibra/surface/__init__.py

@@ -0,0 +1 @@
+from .common import Surface, wrap_return_surface

siibra/surface/common.py

@@ -0,0 +1,77 @@
+from typing import List, Union, IO
+import numpy as np
+import trimesh
+from io import BytesIO
+from functools import wraps
+
+
+class Surface:
+    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.
+
+        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)
+
+        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.vertex_labels) > 0
+        return False
+
+    def __getitem__(self, spec: str):
+        if spec == "verts":
+            return self.vertices
+        if spec == "faces":
+            return self.faces
+        if spec == "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)
+
+    def to_bytes(self):
+        io = BytesIO()
+        mesh = trimesh.Trimesh(self.vertices, self.faces)
+        mesh.export(io, file_obj="obj")
+        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/providers/neuroglancer.py

@@ -18,6 +18,7 @@
 from ...commons import logger, MapType, merge_meshes
 from ...retrieval import requests, cache
 from ...locations import boundingbox as _boundingbox
+from ...surface import wrap_return_surface
 
 from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset
 from neuroglancer_scripts.accessor import get_accessor_for_url
@@ -552,6 +553,7 @@ def _get_fragment_info(self, meshindex: int) -> Dict[str, Tuple[str, ]]:
 
         return result
 
+    @wrap_return_surface()
     def _fetch_fragment(self, url: str, transform_nm: np.ndarray):
         r = requests.HttpRequest(url, func=lambda b: BytesIO(b))
         (vertices_vox, triangles_vox) = read_precomputed_mesh(r.data)

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: