snappy 3.2__cp311-cp311-macosx_10_12_x86_64.whl

snappy/exterior_to_link/barycentric_geometry.py

@@ -0,0 +1,463 @@
+"""
+Defines the basic objects we work with in barycentric coordinates,
+including the various tetrahedron embeddings used for the 2 <--> 3 and
+4 --> 4 moves.
+"""
+
+from ..snap.t3mlite.simplex import *
+from .rational_linear_algebra import Matrix, Vector3, Vector4
+from . import pl_utils
+
+
+class Point():
+    """
+    A point in R^3.  The optional ``boundary`` parameter is for
+    recording the label of the face of a convex polytope containing
+    the point.
+    """
+    def __init__(self, c0, c1, c2, boundary=None):
+        self.vector = Vector3([c0, c1, c2])
+        self._boundary_face = boundary
+
+    def __hash__(self):
+        return hash(self.vector)
+
+    def on_boundary(self):
+        return self._boundary_face is not None
+
+    def boundary_face(self):
+        assert self._boundary_face is not None
+        return self._boundary_face
+
+    def __repr__(self):
+        return self.vector.__repr__()
+
+    def __eq__(self, other):
+        return self.vector == other.vector
+
+    def __ne__(self, other):
+        return self.vector != other.vector
+
+    def to_3d_point(self):
+        return self.vector
+
+    def transform_to_R4(self, matrix):
+        v = Vector4(list(self.vector) + [1])
+        w = matrix * v
+        return BarycentricPoint(*w)
+
+
+class Arc():
+    """
+    A line segment between two Points, often part of a linked list of
+    Arcs forming a PL path or loop.
+    """
+    def __init__(self, start, end, past=None, next=None):
+        self.start = start
+        self.end = end
+        self.past = past
+        self.next = next
+
+    def __hash__(self):
+        return hash((self.start, self.end))
+
+    def __eq__(self, other):
+        return (self.start == other.start) and (self.end == other.end)
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def is_point(self):
+        return self.start == self.end
+
+    def height(self):
+        coeffs = self.start.vector.list() + self.end.vector.list()
+        return max(c.height() for c in coeffs)
+
+    def to_3d_points(self):
+        return (self.start.to_3d_point(), self.end.to_3d_point())
+
+    def transform_to_R4(self, matrix):
+        new_start = self.start.transform_to_R4(matrix)
+        new_end = self.end.transform_to_R4(matrix)
+        return BarycentricArc(new_start, new_end)
+
+    def glue_to(self, next_arc):
+        """
+        Helper method used when concatenating two linked lists of Arcs.
+
+        Assumes self.end == next_arc.start and then makes them the
+        same object.
+        """
+        self.next = next_arc
+        next_arc.past = self
+        next_arc.start = self.end
+
+    def max_denom(self):
+        rationals = list(self.start.vector) + list(self.end.vector)
+        return max([q.denominator() for q in rationals])
+
+
+class BarycentricPoint(Point):
+    """
+    A quadruple of Sage rational numbers whose sum is 1.
+    """
+    def __init__(self, c0, c1, c2, c3):
+        self.vector = Vector4([c0, c1, c2, c3])
+        self._zero_coordinates = [i for i in range(4) if self.vector[i] == 0]
+
+        if sum(self.vector) != 1:
+            raise Exception("Barycentric point doesn't sum to 1")
+
+    def __repr__(self):
+        return self.vector.__repr__()
+
+    def __eq__(self, other):
+        return self.vector == other.vector
+
+    def __ne__(self, other):
+        return self.vector != other.vector
+
+    def __hash__(self):
+        return hash(self.vector)
+
+    def has_negative_coordinate(self):
+        for l in self.vector:
+            if l < 0:
+                return True
+        return False
+
+    def negative_coordinates(self):
+        return [l for l in self.vector if l < 0]
+
+    def zero_coordinates(self):
+        return self._zero_coordinates
+
+    def on_boundary(self):
+        return len(self._zero_coordinates) > 0
+
+    def boundary_face(self):
+        zeros = self._zero_coordinates
+        if len(zeros) != 1:
+            raise GeneralPositionError('Not a generic point on a face')
+        return zeros[0]
+
+    def is_interior(self):
+        return len(self._zero_coordinates) == 0
+
+    def convex_combination(self, other, t):
+        c0,c1,c2,c3 = (1-t)*self.vector + t*other.vector
+        return BarycentricPoint(c0, c1, c2, c3)
+
+    def transform_to_R3(self, matrix, bdry_map=None):
+        v = self.vector
+        new_v = matrix*v
+        boundary_face = None
+        if bdry_map is not None and self.on_boundary():
+            face = self.zero_coordinates()[0]
+            boundary_face = bdry_map[face]
+        return Point(new_v[0], new_v[1], new_v[2], boundary_face)
+
+    def min_nonzero(self):
+        return min([c for c in self.vector if c > 0])
+
+    def to_3d_point(self):
+        return self.vector[0:3]
+
+    def permute(self, perm):
+        """
+        Start with a permutation perm, which represents a map from the
+        vertices of a tetrahedron T in which a point lies, to the
+        vertices of another tetrahedron S which is glued to T. Then,
+        translate the barycentric coordinates of the point in T to the
+        corresponding barycentric coordinates of the point in S.  On
+        the interior, this doesn't make much sense; it really should
+        be used for points on the common boundary triangle.
+        """
+        v = self.vector
+        new_v = [0]*4
+        for i in range(4):
+            new_v[perm[i]] = v[i]
+        return BarycentricPoint(*new_v)
+
+    def round(self, max_denom=2**32, force=False):
+        if force or max(x.denominator() for x in self.vector) > max_denom:
+            v = []
+            for y in max_denom * self.vector:
+                if y != 0:
+                    y = max(y.round(), 1)
+                v.append(y)
+
+            # Should be just Vector4(v)/sum(v)
+            self.vector = Vector4(Vector4(v)/sum(v))
+            self._zero_coordinates = [i for i in range(4) if self.vector[i] == 0]
+
+
+class BarycentricArc(Arc):
+    """
+    A line segment between two endpoints in barycentric coordinates.
+    """
+    def __init__(self, start, end, past=None, next=None, tet=None):
+        self.start = start
+        self.end = end
+        self.past = past
+        self.next = next
+        self.tet = tet
+
+    def __hash__(self):
+        return hash((self.start, self.end, self.tet))
+
+    def __eq__(self, other):
+        return ((self.start == other.start)
+                and (self.end == other.end)
+                and (self.tet == other.tet))
+
+    def trim(self):
+        """
+        Given an arc in R^4 lying in the slice x0 + x1 + x2 + x3 = 1,
+        return its intersection with the standard three-simplex.
+        """
+
+        t0, t1 = 0, 1
+        u, v = self.start.vector, self.end.vector
+        for i in range(4):
+            if u[i] < 0 and v[i] < 0:
+                return None
+            elif u[i] >= 0 and v[i] >= 0:
+                continue
+            else:
+                t = u[i]/(u[i] - v[i])
+                assert (1 - t)*u[i] + t*v[i] == 0
+                if u[i] < 0:
+                    t0 = max(t0, t)
+                else:
+                    t1 = min(t1, t)
+
+        if t1 < t0:
+            return None
+        x = (1 - t0)*u + t0*v
+        y = (1 - t1)*u + t1*v
+        return BarycentricArc(BarycentricPoint(*x), BarycentricPoint(*y))
+
+    def __repr__(self):
+        return '[{},{}]'.format(self.start, self.end)
+
+    def transform_to_R3(self, matrix, bdry_map=None):
+        new_start = self.start.transform_to_R3(matrix, bdry_map)
+        new_end = self.end.transform_to_R3(matrix, bdry_map)
+        return BarycentricArc(new_start, new_end)
+
+    def is_nongeneric(self):
+        zeros_s = self.start.zero_coordinates()
+        zeros_e = self.end.zero_coordinates()
+        if len(zeros_s) > 1 or len(zeros_e) > 1:
+            return True
+        return bool(set(zeros_s) & set(zeros_e))
+
+    def max_denom(self):
+        rationals = list(self.start.vector) + list(self.end.vector)
+        return max(q.denominator() for q in rationals)
+
+
+class InfinitesimalArc(Arc):
+    """
+    A length 0 arc corresponding to moving across a face from one
+    tetrahedron to the adjacent one.
+    """
+    def __init__(self, start, end, start_tet, end_tet, past=None, next=None):
+        self.start, self.end = start, end
+        self.start_tet, self.end_tet = start_tet, end_tet
+        self.past, self.next = past, next
+
+    def __repr__(self):
+        v, i = self.start, self.start_tet
+        w, j = self.end, self.end_tet
+        return f'InfArc({i}:{v}; {j}:{w})'
+
+
+# We consider a bipyramid with a triangular base, i.e. the union of
+# two tetrahedra sharing a face, with vertices A, B, C around the
+# equator and poles N and S.  The orientation convention is that
+# looking down at N the equator is A, B, C in anticlockwise order.
+#
+# Here are Malik's original choices:
+
+# A = vector(QQ, [ 1,  0,  0])
+# B = vector(QQ, [-1,  1,  0])
+# C = vector(QQ, [-1, -1,  0])
+# N = vector(QQ, [ 0,  0,  1])
+# S = vector(QQ, [ 0,  0, -1])
+
+# One subtly is given a second bipyramid (A', B', C', N', S') there
+# are two simple PL homeos between it and (A, B, C, N, S): you can
+# divide them into to two tetrahedra sharing a face, or three
+# tetrahedra around the line joining N to S, and then use the unique
+# affine map between each pair of tetrahedra.  These two PL maps are
+# typically different unless there is a global affine map taking one
+# bipyramid to the other.  It is thus convenient to us a standard
+# bipyramid which is symmetric with respect to affine maps.
+A = Vector3([ 3, 0, 0])
+B = Vector3([ 0, 0, 3])
+C = Vector3([ 0, 3, 0])
+N = Vector3([ 0, 0, 0])
+S = Vector3([ 2, 2, 2])
+
+
+class TetrahedronEmbedding():
+    """
+    A map from a tetrahedron with PL arcs in barycentric coordinates
+    into R^3. The map is described by choosing where the vertices of
+    the given arrow go, in the standard order::
+
+      (tail, head, opp_tail, opp_head)
+
+    The optional boundary information is for recording which faces
+    (if any) of the tetrahedron correspond particular faces of some
+    larger convex polytope.
+    """
+    def __init__(self, arrow, vertex_images, bdry_map=None):
+        opp_arrow = arrow.copy().opposite()
+        to_arrow = {arrow.tail():0, arrow.head():1,
+                    opp_arrow.tail():2, opp_arrow.head():3}
+        self.vertex_images = [vertex_images[to_arrow[V]] for V in ZeroSubsimplices]
+        if bdry_map is not None:
+            bdry_map = {i:bdry_map[to_arrow[V]] for i, V in enumerate(ZeroSubsimplices)}
+        self.bdry_map = bdry_map
+        assert [len(v) for v in vertex_images] == 4*[3]
+        R4_images = [list(v) + [1] for v in self.vertex_images]
+        self.matrix = Matrix(R4_images).transpose()
+        self.inverse_matrix = self.matrix.inverse()
+        # assert self.matrix.det() > 0 # disabled for speed
+
+    def transfer_arcs_to_R3(self, arcs):
+        return [arc.transform_to_R3(self.matrix, bdry_map=self.bdry_map) for arc in arcs]
+
+    def transfer_arcs_from_R3(self, arcs):
+        return [arc.transform_to_R4(self.inverse_matrix) for arc in arcs]
+
+    def info(self):
+        self.tetrahedron.info()
+        print(self.matrix)
+
+
+class TetrahedronEmbeddingCache():
+    def __init__(self):
+        self.cache = {}
+
+    def __call__(self, arrow, vertex_images, bdry_map=None):
+        if bdry_map is None:
+            bdry_map_key = None
+        else:
+            bdry_map_key = tuple(bdry_map)
+        key = (arrow.Edge, arrow.Face, tuple(vertex_images), bdry_map_key)
+        if key not in self.cache:
+            self.cache[key] = TetrahedronEmbedding(arrow, vertex_images, bdry_map)
+        return self.cache[key]
+
+
+tetrahedron_embedding = TetrahedronEmbeddingCache()
+
+
+def barycentric_face_embedding(arrow, north_pole=None):
+    """
+    The arrow here is a directed edge in a specified tetrahedron.  It
+    also specifies a face (the face which is disjoint from the arrow,
+    except for the head).  This helper function takes the arrow and
+    embeds the face of the arrow in the xy-plane, with the two
+    tetrahedra on either side of the face embedded in the upper and
+    lower half-spaces.  The specific coordinates are labeled below; A,
+    B, and C are the vertices of the image of the face in the
+    xy-plane, and N and S are images of the vertices of the two
+    tetrahedron not in the face.
+    """
+    if north_pole is None:
+        north_pole = N
+    next_arrow = arrow.glued()
+    top_bdry = [None, 't1', 't2', 't3']
+    bottom_brdy = ['b1', None, 'b2', 'b3']
+
+    emb_top = tetrahedron_embedding(arrow, [north_pole, A, C, B], top_bdry)
+    emb_bottom = tetrahedron_embedding(next_arrow, [A, S, C, B], bottom_brdy)
+
+    return [(arrow.Tetrahedron, emb_top),
+            (next_arrow.Tetrahedron, emb_bottom)]
+
+
+def barycentric_edge_embedding(arrow, north_pole=None):
+    """
+    Take the arrow corresponding to an edge of valence 3. This
+    function then creates an embedding of the three tetrahedra glued
+    in pairs around the edge into R^3. The embedding is defined so
+    that the edge goes from N to S, as labeled below, The arrow goes
+    from A to B; A, B, and C form a triangle in the xy-plane.
+
+    Note that this arrangement has the same image in R^3 as the
+    barycentric_face_embedding above -- that's by design, so that we
+    can use these two maps to transfer the arcs in barycentric
+    coordinates under two-three and two-three moves.
+    """
+    if north_pole is None:
+        north_pole = N
+    assert len(arrow.linking_cycle()) == 3
+    arrow = arrow.copy()
+    verts = [A, B, C, A]
+    ans = []
+    for i in range(3):
+        tet_verts = [verts[i], verts[i+1], S, north_pole]
+        bdry_map = [None, None, f't{i+1}', f'b{i+1}']
+        ans.append((arrow.Tetrahedron,
+                    tetrahedron_embedding(arrow, tet_verts, bdry_map)))
+        arrow.next()
+    return ans
+
+
+# arrow, tail, head, opp_tail, opp_head
+def barycentric_quad_embedding0(arrow, north_pole=None):
+    """
+    Take an arrow with 4 valent axis, then build embedding of the
+    surrounding four tetrahedra forming an octahedron in R^3 using the
+    arrows running around the valence 4 edge in xy plane.
+    """
+    n = Vector3([ 0, 0, 1]) if north_pole is None else north_pole
+    e = Vector3([ 1, 0, 0])
+    s = Vector3([ 0, 0,-1])
+    w = Vector3([-1, 0, 0])
+    a = Vector3([ 0,-1, 0])
+    b = Vector3([ 0, 1, 0])
+
+    arrow = arrow.copy()
+    ans = []
+    verts = [e, b, w, a, e]
+    for i in range(4):
+        bdry_map = [None, None, f'x{i}', f'y{i}']
+        tet_verts = [verts[i], verts[i + 1], s, n]
+        ans.append((arrow.Tetrahedron,
+                    tetrahedron_embedding(arrow, tet_verts, bdry_map)))
+        arrow.next()
+
+    return ans
+
+
+# arrow, tail, head, opp_tail, opp_head
+def barycentric_quad_embedding1(arrow, north_pole=None):
+    """
+    Take an arrow with 4 valent axis, then build embedding of the
+    surrounding four tetrahedra forming an octahedron in R^3 using the
+    arrows running around the valence 4 edge in zy plane.
+    """
+    n = Vector3([ 0, 0, 1]) if north_pole is None else north_pole
+    e = Vector3([ 1, 0, 0])
+    s = Vector3([ 0, 0,-1])
+    w = Vector3([-1, 0, 0])
+    a = Vector3([ 0,-1, 0])
+    b = Vector3([ 0, 1, 0])
+
+    arrow = arrow.copy()
+    ans = []
+    verts = [e, s, w, n, e]
+    for i in range(4):
+        ans.append((arrow.Tetrahedron,
+                    tetrahedron_embedding(arrow, [verts[i], verts[i+1], a, b])))
+        arrow.next()
+
+    return ans

snappy/exterior_to_link/exceptions.py

@@ -0,0 +1,6 @@
+class GeneralPositionError(Exception):
+    pass
+
+
+class ExteriorToLinkError(Exception):
+    pass