diff --git a/environment_dev.yml b/environment_dev.yml index 2cb5dbd..918b1e4 100644 --- a/environment_dev.yml +++ b/environment_dev.yml @@ -55,4 +55,3 @@ dependencies: - setuptools-scm==7.1.0 - snirf==0.7.4 - pmcx - - open3d==0.16 diff --git a/src/cedalion/dataclasses/geometry.py b/src/cedalion/dataclasses/geometry.py index 364fd78..2569128 100644 --- a/src/cedalion/dataclasses/geometry.py +++ b/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": diff --git a/src/cedalion/imagereco/forward_model.py b/src/cedalion/imagereco/forward_model.py index b01b759..4c86bcc 100644 --- a/src/cedalion/imagereco/forward_model.py +++ b/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