improve triangulation and LearnerND typing

Author: basnijholt

adaptive/learner/learnerND.py

@@ -40,7 +40,7 @@ def volume(simplex: List[Tuple[float, float]], ys: None = None,) -> float:
     return vol
 
 
-def orientation(simplex):
+def orientation(simplex: np.ndarray):
     matrix = np.subtract(simplex[:-1], simplex[-1])
     # See https://www.jstor.org/stable/2315353
     sign, _logdet = np.linalg.slogdet(matrix)

adaptive/learner/triangulation.py

@@ -1,14 +1,18 @@
+import collections.abc
 import math
 from collections import Counter
-from collections.abc import Iterable, Sized
 from itertools import chain, combinations
 from math import factorial
-from typing import Any, Iterator, List, Optional, Sequence, Set, Tuple, Union
+from typing import Any, Iterable, Iterator, List, Optional, Sequence, Set, Tuple, Union
 
 import numpy as np
 import scipy.spatial
 
-Simplex = Tuple[int, ...]  # XXX: check if this is correct
+SimplexPoints = Union[
+    List[Tuple[float, ...]], np.ndarray
+]  # XXX: check if this is correct
+Simplex = Tuple[int, ...]
+Point = Union[Tuple[float, ...], np.ndarray]  # XXX: check if this is correct
 
 
 def fast_norm(v: Union[Tuple[float, ...], np.ndarray]) -> float:
@@ -21,9 +25,7 @@ def fast_norm(v: Union[Tuple[float, ...], np.ndarray]) -> float:
 
 
 def fast_2d_point_in_simplex(
-    point: Tuple[float, ...],
-    simplex: Union[List[Tuple[float, ...]], np.ndarray],
-    eps: float = 1e-8,
+    point: Point, simplex: SimplexPoints, eps: float = 1e-8
 ) -> Union[bool, np.bool_]:
     (p0x, p0y), (p1x, p1y), (p2x, p2y) = simplex
     px, py = point
@@ -38,9 +40,7 @@ def fast_2d_point_in_simplex(
     return (t >= -eps) and (s + t <= 1 + eps)
 
 
-def point_in_simplex(
-    point: Any, simplex: Simplex, eps: float = 1e-8
-) -> Union[bool, np.bool_]:
+def point_in_simplex(point: Point, simplex: SimplexPoints, eps: float = 1e-8) -> bool:
     if len(point) == 2:
         return fast_2d_point_in_simplex(point, simplex, eps)
 
@@ -51,7 +51,7 @@ def point_in_simplex(
     return all(alpha > -eps) and sum(alpha) < 1 + eps
 
 
-def fast_2d_circumcircle(points: np.ndarray,) -> Tuple[Tuple[float, float], float]:
+def fast_2d_circumcircle(points: Iterable[Point]) -> Tuple[Tuple[float, float], float]:
     """Compute the center and radius of the circumscribed circle of a triangle
 
     Parameters
@@ -88,7 +88,7 @@ def fast_2d_circumcircle(points: np.ndarray,) -> Tuple[Tuple[float, float], floa
 
 
 def fast_3d_circumcircle(
-    points: np.ndarray,
+    points: Iterable[Point],
 ) -> Tuple[Tuple[float, float, float], float]:
     """Compute the center and radius of the circumscribed shpere of a simplex.
 
@@ -140,7 +140,7 @@ def fast_det(matrix: np.ndarray) -> float:
         return np.linalg.det(matrix)
 
 
-def circumsphere(pts: np.ndarray,) -> Tuple[Tuple[float, ...], float]:
+def circumsphere(pts: np.ndarray) -> Tuple[Tuple[float, ...], float]:
     dim = len(pts) - 1
     if dim == 2:
         return fast_2d_circumcircle(pts)
@@ -193,10 +193,12 @@ def orientation(face: np.ndarray, origin: np.ndarray) -> int:
 
 
 def is_iterable_and_sized(obj: Any) -> bool:
-    return isinstance(obj, Iterable) and isinstance(obj, Sized)
+    return isinstance(obj, collections.abc.Iterable) and isinstance(
+        obj, collections.abc.Sized
+    )
 
 
-def simplex_volume_in_embedding(vertices: List[Tuple[float, ...]]) -> float:
+def simplex_volume_in_embedding(vertices: Iterable[Point]) -> float:
     """Calculate the volume of a simplex in a higher dimensional embedding.
     That is: dim > len(vertices) - 1. For example if you would like to know the
     surface area of a triangle in a 3d space.
@@ -277,7 +279,7 @@ class Triangulation:
         or more simplices in the
     """
 
-    def __init__(self, coords: np.ndarray) -> None:
+    def __init__(self, coords: Iterable[Point]) -> None:
         if not is_iterable_and_sized(coords):
             raise TypeError("Please provide a 2-dimensional list of points")
         coords = list(coords)
@@ -305,10 +307,10 @@ def __init__(self, coords: np.ndarray) -> None:
                 "(the points are linearly dependent)"
             )
 
-        self.vertices = list(coords)
-        self.simplices = set()
+        self.vertices: List[Point] = list(coords)
+        self.simplices: Set[Simplex] = set()
         # initialise empty set for each vertex
-        self.vertex_to_simplices = [set() for _ in coords]
+        self.vertex_to_simplices: List[Set[Simplex]] = [set() for _ in coords]
 
         # find a Delaunay triangulation to start with, then we will throw it
         # away and continue with our own algorithm
@@ -328,16 +330,16 @@ def add_simplex(self, simplex: Simplex) -> None:
         for vertex in simplex:
             self.vertex_to_simplices[vertex].add(simplex)
 
-    def get_vertices(self, indices: Sequence[int]) -> Any:
+    def get_vertices(self, indices: Sequence[int]) -> List[Optional[Point]]:
         return [self.get_vertex(i) for i in indices]
 
-    def get_vertex(self, index: Optional[int]) -> Any:
+    def get_vertex(self, index: Optional[int]) -> Optional[Point]:
         if index is None:
             return None
         return self.vertices[index]
 
     def get_reduced_simplex(
-        self, point: Any, simplex: Simplex, eps: float = 1e-8
+        self, point: Point, simplex: Simplex, eps: float = 1e-8
     ) -> list:
         """Check whether vertex lies within a simplex.
 
@@ -364,12 +366,12 @@ def get_reduced_simplex(
         return [simplex[i] for i in result]
 
     def point_in_simplex(
-        self, point: Any, simplex: Simplex, eps: float = 1e-8
-    ) -> Union[bool, np.bool_]:
+        self, point: Point, simplex: Simplex, eps: float = 1e-8
+    ) -> bool:
         vertices = self.get_vertices(simplex)
         return point_in_simplex(point, vertices, eps)
 
-    def locate_point(self, point: Any) -> Any:
+    def locate_point(self, point: Point) -> Simplex:
         """Find to which simplex the point belongs.
 
         Return indices of the simplex containing the point.
@@ -385,8 +387,11 @@ def dim(self) -> int:
         return len(self.vertices[0])
 
     def faces(
-        self, dim: None = None, simplices: Optional[Any] = None, vertices: None = None
-    ) -> Iterator[Any]:
+        self,
+        dim: Optional[int] = None,
+        simplices: Optional[Iterable[Simplex]] = None,
+        vertices: Optional[Iterable[int]] = None,
+    ) -> Iterator[Tuple[int, ...]]:
         """Iterator over faces of a simplex or vertex sequence."""
         if dim is None:
             dim = self.dim
@@ -407,11 +412,11 @@ def faces(
         else:
             return faces
 
-    def containing(self, face):
+    def containing(self, face: Tuple[int, ...]) -> Set[Simplex]:
         """Simplices containing a face."""
         return set.intersection(*(self.vertex_to_simplices[i] for i in face))
 
-    def _extend_hull(self, new_vertex: Any, eps: float = 1e-8) -> Any:
+    def _extend_hull(self, new_vertex: Point, eps: float = 1e-8) -> Set[Simplex]:
         # count multiplicities in order to get all hull faces
         multiplicities = Counter(face for face in self.faces())
         hull_faces = [face for face, count in multiplicities.items() if count == 1]
@@ -471,7 +476,7 @@ def circumscribed_circle(
 
     def point_in_cicumcircle(
         self, pt_index: int, simplex: Simplex, transform: np.ndarray
-    ) -> np.bool_:
+    ) -> bool:
         # return self.fast_point_in_circumcircle(pt_index, simplex, transform)
         eps = 1e-8
 
@@ -487,9 +492,9 @@ def default_transform(self) -> np.ndarray:
     def bowyer_watson(
         self,
         pt_index: int,
-        containing_simplex: Optional[Any] = None,
+        containing_simplex: Optional[Simplex] = None,
         transform: Optional[np.ndarray] = None,
-    ) -> Any:
+    ) -> Tuple[Set[Simplex], Set[Simplex]]:
         """Modified Bowyer-Watson point adding algorithm.
 
         Create a hole in the triangulation around the new point,
@@ -549,7 +554,7 @@ def bowyer_watson(
         new_triangles = self.vertex_to_simplices[pt_index]
         return bad_triangles - new_triangles, new_triangles - bad_triangles
 
-    def _simplex_is_almost_flat(self, simplex: Simplex) -> np.bool_:
+    def _simplex_is_almost_flat(self, simplex: Simplex) -> bool:
         return self._relative_volume(simplex) < 1e-8
 
     def _relative_volume(self, simplex: Simplex) -> float:
@@ -565,8 +570,8 @@ def _relative_volume(self, simplex: Simplex) -> float:
 
     def add_point(
         self,
-        point: Any,
-        simplex: Optional[Any] = None,
+        point: Point,
+        simplex: Optional[Simplex] = None,
         transform: Optional[np.ndarray] = None,
     ) -> Any:
         """Add a new vertex and create simplices as appropriate.
@@ -575,13 +580,13 @@ def add_point(
         ----------
         point : float vector
             Coordinates of the point to be added.
-        transform : N*N matrix of floats
-            Multiplication matrix to apply to the point (and neighbouring
-            simplices) when running the Bowyer Watson method.
         simplex : tuple of ints, optional
             Simplex containing the point. Empty tuple indicates points outside
             the hull. If not provided, the algorithm costs O(N), so this should
             be used whenever possible.
+        transform : N*N matrix of floats
+            Multiplication matrix to apply to the point (and neighbouring
+            simplices) when running the Bowyer Watson method.
         """
         point = tuple(point)
         if simplex is None:
@@ -626,7 +631,7 @@ def volume(self, simplex: Simplex) -> float:
     def volumes(self) -> List[float]:
         return [self.volume(sim) for sim in self.simplices]
 
-    def reference_invariant(self):
+    def reference_invariant(self) -> bool:
         """vertex_to_simplices and simplices are compatible."""
         for vertex in range(len(self.vertices)):
             if any(vertex not in tri for tri in self.vertex_to_simplices[vertex]):
@@ -640,26 +645,28 @@ def vertex_invariant(self, vertex):
         """Simplices originating from a vertex don't overlap."""
         raise NotImplementedError
 
-    def get_neighbors_from_vertices(self, simplex: Simplex) -> Any:
+    def get_neighbors_from_vertices(self, simplex: Simplex) -> Set[Simplex]:
         return set.union(*[self.vertex_to_simplices[p] for p in simplex])
 
-    def get_face_sharing_neighbors(self, neighbors: Any, simplex: Simplex) -> Any:
+    def get_face_sharing_neighbors(
+        self, neighbors: Set[Simplex], simplex: Simplex
+    ) -> Set[Simplex]:
         """Keep only the simplices sharing a whole face with simplex."""
         return {
             simpl for simpl in neighbors if len(set(simpl) & set(simplex)) == self.dim
         }  # they share a face
 
-    def get_simplices_attached_to_points(self, indices: Any) -> Any:
+    def get_simplices_attached_to_points(self, indices: Simplex) -> Set[Simplex]:
         # Get all simplices that share at least a point with the simplex
         neighbors = self.get_neighbors_from_vertices(indices)
         return self.get_face_sharing_neighbors(neighbors, indices)
 
-    def get_opposing_vertices(self, simplex: Simplex,) -> Any:
+    def get_opposing_vertices(self, simplex: Simplex) -> Tuple[int, ...]:
         if simplex not in self.simplices:
             raise ValueError("Provided simplex is not part of the triangulation")
         neighbors = self.get_simplices_attached_to_points(simplex)
 
-        def find_opposing_vertex(vertex):
+        def find_opposing_vertex(vertex: int):
             # find the simplex:
             simp = next((x for x in neighbors if vertex not in x), None)
             if simp is None: