Rename SurfaceGeometry to TriangularMesh

nipy · effigies · Sep 17, 2021 · Sep 29, 2021 · Oct 8, 2021 · Oct 8, 2021
commit 3f62a80250fa2f6363bd678a6c16d71e002cdaed
diff --git a/doc/source/devel/biaps/biap_0009.rst b/doc/source/devel/biaps/biap_0009.rst
@@ -129,7 +129,7 @@ The basic API is as follows:
             """ Nx3 array of coordinates in RAS+ space """
 
 
-    class SurfaceGeometry(Geometry):
+    class TriangularMesh(Geometry):
         @property
         def n_triangles(self):
             """ Number of faces """
@@ -146,7 +146,7 @@ The basic API is as follows:
             """
 
         def decimate(self, *, n_coords=None, ratio=None):
-            """ Return a SurfaceHeader with a smaller number of vertices that
+            """ Return a TriangularMesh with a smaller number of vertices that
             preserves the geometry of the original """
             # To be overridden when a format provides optimization opportunities
 

diff --git a/nibabel/surfaceimages.py b/nibabel/surfaceimages.py
@@ -38,9 +38,12 @@ def n_coords(self):
         """
         return self.get_coords().shape[0]
 
-class SurfaceGeometry(Pointset):
+
+class TriangularMesh(Pointset):
+    """ A triangular mesh is a description of a surface tesselated into triangles """
+
     def __init__(self, meshes=None):
-        """ Surface header objects have access to an internal
+        """ Triangular mesh objects have access to an internal
         ``_meshes`` dictionary that has keys that are mesh names.
         The values may be any structure that permits the class to
         provide coordinates and triangles on request.
@@ -73,7 +76,7 @@ def get_names(self):
         return list(self._meshes.keys())
 
     def decimate(self, *, ncoords=None, ratio=None):
-        """ Return a SurfaceHeader with a smaller number of vertices that
+        """ Return a TriangularMesh with a smaller number of vertices that
         preserves the geometry of the original.
 
         Please contribute a generic decimation algorithm at
@@ -93,7 +96,7 @@ def load_face_data(self, pathlike):
 class SurfaceHeader(FileBasedHeader):
     """ Template class to implement SurfaceHeader protocol """
     def get_geometry(self):
-        """ Generate ``SurfaceGeometry`` object from header object
+        """ Generate ``TriangularMesh`` object from header object
 
         If no default geometry can be provided, returns ``None``.
         """
@@ -157,7 +160,7 @@ def from_spec(klass, pathlike):
         raise NotImplementedError
 
 
-class GeometrySequence(GeometryCollection, Pointset):
+class PointsetSequence(GeometryCollection, Pointset):
     def __init__(self, structures=()):
         super().__init__(structures)
         self._indices = {}

diff --git a/nibabel/tests/test_surfaceimages.py b/nibabel/tests/test_surfaceimages.py
@@ -45,7 +45,7 @@ def __slicer__(self, slicer):
             return h5f[self.dataset_name][slicer]
 
 
-class H5Geometry(SurfaceGeometry):
+class H5Geometry(TriangularMesh):
     """Simple Geometry file structure that combines a single topology
     with one or more coordinate sets
     """
@@ -57,7 +57,6 @@ def from_filename(klass, pathlike):
             for name, coords in h5f['coordinates'].items():
                 meshes[name] = (coords, triangles)
         return klass(meshes)
-
 
     def to_filename(self, pathlike):
         topology = None
@@ -75,14 +74,12 @@ def to_filename(self, pathlike):
             for name, coord in coordinates.items():
                 h5f.create_dataset(f"/coordinates/{name}", coord)
 
-
     def get_coords(self, name=None):
         if name is None:
             name = next(iter(self._meshes))
         coords, _ = self._meshes[name]
         return coords
 
-
     def get_triangles(self, name=None):
         if name is None:
             name = next(iter(self._meshes))
@@ -163,7 +160,7 @@ def triangles(self):
         return ap
 
 
-class FreeSurferHemisphere(SurfaceGeometry):
+class FreeSurferHemisphere(TriangularMesh):
     @classmethod
     def from_filename(klass, pathlike):
         path = Path(pathlike)