ENH: Add stubs from BIAP 9

Author: effigies

nibabel/coordimage.py

@@ -0,0 +1,61 @@
+class CoordinateImage:
+    """
+    Attributes
+    ----------
+    header : a file-specific header
+    coordaxis : ``CoordinateAxis``
+    dataobj : array-like
+    """
+
+
+class CoordinateAxis:
+    """
+    Attributes
+    ----------
+    parcels : list of ``Parcel`` objects
+    """
+
+    def load_structures(self, mapping):
+        """
+        Associate parcels to ``Pointset`` structures
+        """
+        raise NotImplementedError
+
+    def __getitem__(self, slicer):
+        """
+        Return a sub-sampled CoordinateAxis containing structures
+        matching the indices provided.
+        """
+        raise NotImplementedError
+
+    def get_indices(self, parcel, indices=None):
+        """
+        Return the indices in the full axis that correspond to the
+        requested parcel. If indices are provided, further subsample
+        the requested parcel.
+        """
+        raise NotImplementedError
+
+
+class Parcel:
+    """
+    Attributes
+    ----------
+    name : str
+    structure : ``Pointset``
+    indices : object that selects a subset of coordinates in structure
+    """
+
+
+class GeometryCollection:
+    """
+    Attributes
+    ----------
+    structures : dict
+        Mapping from structure names to ``Pointset``
+    """
+
+    @classmethod
+    def from_spec(klass, pathlike):
+        """Load a collection of geometries from a specification."""
+        raise NotImplementedError

nibabel/pointset.py

@@ -0,0 +1,56 @@
+class Pointset:
+    @property
+    def n_coords(self):
+        """Number of coordinates
+
+        Subclasses should override with more efficient implementations.
+        """
+        return len(self.get_coords())
+
+    def get_coords(self, name=None):
+        """Nx3 array of coordinates in RAS+ space"""
+        raise NotImplementedError
+
+
+class TriangularMesh(Pointset):
+    @property
+    def n_triangles(self):
+        """Number of faces
+
+        Subclasses should override with more efficient implementations.
+        """
+        return len(self.get_triangles())
+
+    def get_triangles(self, name=None):
+        """Mx3 array of indices into coordinate table"""
+        raise NotImplementedError
+
+    def get_mesh(self, name=None):
+        return self.get_coords(name=name), self.get_triangles(name=name)
+
+    def get_names(self):
+        """List of surface names that can be passed to
+        ``get_{coords,triangles,mesh}``
+        """
+        raise NotImplementedError
+
+    ## This method is called for by the BIAP, but it now seems simpler to wait to
+    ## provide it until there are any proposed implementations
+    # def decimate(self, *, n_coords=None, ratio=None):
+    #     """ 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
+    #     raise NotImplementedError
+
+
+class NdGrid(Pointset):
+    """
+    Attributes
+    ----------
+    shape : 3-tuple
+        number of coordinates in each dimension of grid
+    """
+
+    def get_affine(self, name=None):
+        """4x4 array"""
+        raise NotImplementedError