change surface mesh decimation to vtk based algorithm

environment_dev.yml

@@ -55,4 +55,3 @@ dependencies:
       - setuptools-scm==7.1.0
       - snirf==0.7.4
       - pmcx
-      - open3d==0.16

src/cedalion/dataclasses/geometry.py

@@ -8,6 +8,7 @@
 import pint
 import trimesh
 import vtk
+import mne
 import xarray as xr
 from scipy.spatial import KDTree
 from vtk.util.numpy_support import vtk_to_numpy
@@ -129,12 +130,11 @@ def decimate(self, face_count: int) -> "TrimeshSurface":
             The surface with a decimated mesh
         """
 
-        try:
-            decimated = self.mesh.simplify_quadric_decimation(face_count)
-        except:
-            # deprecated trimesh function, please update trimesh!
-            decimated = self.mesh.simplify_quadratic_decimation(face_count)
-
+        vertices, faces = mne.decimate_surface(self.mesh.vertices,
+                                               self.mesh.faces, face_count,
+                                               method="quadric")
+        decimated = trimesh.Trimesh(vertices, faces)
+
         return TrimeshSurface(decimated, self.crs, self.units)
 
     def smooth(self, lamb: float) -> "TrimeshSurface":

src/cedalion/imagereco/forward_model.py

@@ -27,7 +27,7 @@ class TwoSurfaceHeadModel:
     segmentation_masks: xr.DataArray
     brain: cdc.Surface
     scalp: cdc.Surface
-    landmarks: Optional[cdt.LabledPointCloud]
+    landmarks: Optional[cdt.LabeledPointCloud]
     t_ijk2ras: cdt.AffineTransform
     t_ras2ijk: cdt.AffineTransform
     voxel_to_vertex_brain: scipy.sparse.spmatrix