Merge pull request #411 from Deep-MI/parc

use nibabel read_geometry

recon_surf/rewrite_mc_surface.py

@@ -18,7 +18,6 @@
 import optparse
 import nibabel.freesurfer.io as fs
 from nibabel import load as nibload
-from lapy._read_geometry import read_geometry
 
 
 def options_parse():
@@ -69,7 +68,7 @@ def resafe_surface(insurf: str, outsurf: str, pretess: str) -> None:
         Path and name of file the input surface was created on (e.g. filled-pretess127.mgz)
     
     """
-    surf = read_geometry(insurf, read_metadata=True)
+    surf = fs.read_geometry(insurf, read_metadata=True)
 
     if not surf[2]["filename"]:
         # Set information with file used for surface construction (volume info and name)

recon_surf/smooth_aparc.py

@@ -22,7 +22,6 @@
 import numpy as np
 from numpy import typing as npt
 import nibabel.freesurfer.io as fs
-from lapy._read_geometry import read_geometry
 from scipy import sparse
 
 
@@ -269,7 +268,7 @@ def smooth_aparc(
     """
     # read input files
     print("Reading in surface: {} ...".format(insurfname))
-    surf = read_geometry(insurfname, read_metadata=True)
+    surf = fs.read_geometry(insurfname, read_metadata=True)
     print("Reading in annotation: {} ...".format(inaparcname))
     aparc = fs.read_annot(inaparcname)
     print("Reading in cortex label: {} ...".format(incortexname))

recon_surf/spherically_project.py

@@ -21,7 +21,6 @@
 import math
 from lapy.diffGeo import tria_mean_curvature_flow
 from lapy.triaMesh import TriaMesh
-from lapy.read_geometry import read_geometry
 from lapy.solver import Solver
 
 HELPTEXT = """
@@ -320,7 +319,7 @@ def spherically_project_surface(
         Try to use the Cholesky decomposition from the cholmod. Defaults to True
 
     """
-    surf = read_geometry(insurf, read_metadata=True)
+    surf = fs.read_geometry(insurf, read_metadata=True)
     projected = tria_spherical_project(
         TriaMesh(surf[0], surf[1]), flow_iter=3, use_cholmod=use_cholmod
     )