snappy 3.2__cp310-cp310-macosx_10_12_x86_64.whl

snappy/ptolemy/fieldExtensions.py

@@ -0,0 +1,153 @@
+from .polynomial import Polynomial, Monomial
+from . import matrix
+
+
+def my_rnfequation(base_poly, extension_poly):
+    """
+    This is returning the same as pari's
+    rnfequation(base_poly, extension_poly, flag = 3) but
+    assumes that base_poly and extension_poly are irreducible
+    and thus is much faster.
+    """
+
+    # Get the degrees of the polynomial and the variables they are in
+
+    # Example: base_poly t^2 + 1, extension_poly s^3 + t
+
+    base_vars = base_poly.variables()
+    assert len(base_vars) == 1
+    base_var = base_vars[0]                                 # would be y
+    base_degree = base_poly.degree()                        # would be 2
+    assert base_degree > 1
+
+    extension_vars = extension_poly.variables()
+    extra_vars = set(extension_vars) - set(base_vars)
+    assert len(extra_vars) == 1
+    extension_var = list(extra_vars)[0]                     # would be x
+    extension_degree = extension_poly.degree(extension_var) # would be 3
+    assert extension_degree > 1
+
+    # total degree
+    total_degree = base_degree * extension_degree
+
+    # If the extension_poly does not contain base_var, e.g.,
+    # s^2 + 1 and t^2 - 2, then we know that neither s nor t will
+    # generate the entire field, so skip k = 0
+    start_k = 0 if base_var in extension_vars else -1
+
+    # Try different k to find a generator for the total field
+    for k in range(start_k, -100, -1):
+
+        # Use x = s + k * t as potential generator
+
+        x = (  Polynomial.from_variable_name(extension_var)
+                   + Polynomial.constant_polynomial(k) *
+                     Polynomial.from_variable_name(base_var))
+
+        # Holds the i-th power of x in the reduced form
+
+        power_of_x = Polynomial.constant_polynomial(1)
+
+        # The i-th row holds the coefficient of the polynomial
+        # obtained by reducing the i-th power with respect to the
+        # Groebner basis
+
+        mat = [ ]
+
+        for i in range(total_degree):
+
+            # Add to matrix
+
+            mat.append(
+                _poly_to_row(power_of_x,
+                             base_var, base_degree,
+                             extension_var, extension_degree))
+
+            # Compute next power
+
+            power_of_x = (
+                _reduced_polynomial(
+                    _reduced_polynomial(power_of_x * x,
+                                        extension_poly,
+                                        extension_var,
+                                        extension_degree),
+                    base_poly,
+                    base_var,
+                    base_degree))
+
+        row_largest_power = _poly_to_row(
+            power_of_x,
+            base_var, base_degree, extension_var, extension_degree)
+
+        try:
+            mat_inv = matrix.matrix_inverse(mat)
+        except Exception as e:
+            if not matrix.matrix_determinant(mat) == 0:
+                raise e
+        else:
+            mat_inv_t = matrix.matrix_transpose(mat_inv)
+
+            new_poly_1 = _row_to_poly(
+                matrix.matrix_mult_vector(
+                    mat_inv_t,
+                    row_largest_power))
+            new_poly_2 = Polynomial.from_variable_name('x') ** total_degree
+            new_poly = new_poly_2 - new_poly_1
+
+            old_var_in_new_var = _row_to_poly(
+                matrix.matrix_mult_vector(
+                    mat_inv_t,
+                    [0, 1] + (total_degree - 2) * [0]))
+
+            return new_poly, old_var_in_new_var, k
+
+    raise Exception("Should not get here")
+
+
+def _row_to_poly(row):
+    zero = Polynomial.constant_polynomial(0)
+    x = Polynomial.from_variable_name('x')
+    return sum([ Polynomial.constant_polynomial(c) * x ** i
+                 for i, c in enumerate(row)],
+               zero)
+
+
+def _poly_to_row(poly, base_var, base_degree, extension_var, extension_degree):
+    row = base_degree * extension_degree * [ 0 ]
+    for m in poly.get_monomials():
+        degrees = dict(m.get_vars())
+        degree1 = degrees.get(base_var, 0)
+        degree2 = degrees.get(extension_var, 0)
+        index = degree2 * base_degree + degree1
+        row[index] = m.get_coefficient()
+    return row
+
+
+def _reduced_polynomial(poly, mod_pol, mod_var, mod_degree):
+
+    def degree_of_monomial(m):
+        vars = dict(m.get_vars())
+        return vars.get(mod_var, 0)
+
+    def reducing_polynomial(m):
+        def new_degree(var, expo):
+            if var == mod_var:
+                return (var, expo - mod_degree)
+            else:
+                return (var, expo)
+        new_degrees = [ new_degree(var, expo)
+                        for var, expo in m.get_vars() ]
+        new_degrees_filtered = tuple([ (var, expo)
+                                       for var, expo in new_degrees
+                                       if expo > 0 ])
+        monomial = Monomial(m.get_coefficient(), new_degrees_filtered)
+        return Polynomial((monomial,))
+
+    while True:
+        degree = poly.degree(mod_var)
+        if degree < mod_degree:
+            return poly
+
+        for m in poly.get_monomials():
+            if degree_of_monomial(m) == degree:
+                poly = poly - reducing_polynomial(m) * mod_pol

snappy/ptolemy/findLoops.py

@@ -0,0 +1,473 @@
+from . import matrix
+
+# Given a SnapPy Manifold, find loops of short, middle, and long edges of the
+# doubly truncated simplices that represent the generators of the fundamental
+# group in the unsimplified presentation.
+
+# We construct a fundamental domain of the Manifold from doubly truncated
+# simplices. See Figure 18 for simplices.
+#    Garoufalidis, Goerner, Zickert:
+#    Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+#    https://arxiv.org/abs/1207.6711
+
+# We use SnapPy's _choose_generators_info to construct the same fundamental
+# domain and side pairing that SnapPy uses for the unsimplified fundamental
+# group presentation.
+
+# We then pick a vertex of one doubly truncated simplex as origin and compute
+# for each vertex a shortest path from the origin to that vertex.
+
+# For each face marked as outbound_generator, pick a vertex on the face and
+# a path from the origin to that vertex. Then, the side pairing gives a
+# corresponding face on an inbound_generator, pick a path to the corresponding
+# vertex. Compute the first path with the inverse of the second.
+# There are six such choices for each outbound_generator face. Pick the one
+# yielding the shortest loop (in terms of number of short and long edges).
+
+
+class Vertex(tuple):
+    """
+    A triple (tet, v0, v1, v2) representing a vertex of a doubly truncated
+    simplex.
+    v0, v1, and v2 are distinct integers between 0 and 3 (inclusively).
+    As in the paper, it denotes the vertex that is closest to vertex v0 of
+    the simplex, closest to the edge v0 v1 of the simplex and on the face
+    v0 v1 v2 of the simplex.
+    """
+
+    def __new__(cls, tet, v0, v1, v2):
+        return super().__new__(cls, (tet, v0, v1, v2))
+
+    def edges_starting_at_vertex(self):
+        """
+        Return the three edges of the simplex starting at this point.
+        """
+
+        return [ ShortEdge(self), MiddleEdge(self), LongEdge(self) ]
+
+    def __repr__(self):
+        return "Vertex(%d,%d,%d,%d)" % self
+
+
+class Edge():
+    """
+    Base class representing a directed edge of the doubly truncated
+    simplex.
+    """
+
+    def __init__(self, start_point):
+        """
+        Constructs an edge starting at the given start_point which is
+        of type Vertex.
+        """
+        self._start_point = start_point
+
+    def start_point(self):
+        """
+        The Vertex object that is the start point of edge.
+        """
+        return self._start_point
+
+    def __pow__(self, other):
+        """
+        Invert an edge with ** -1
+        """
+        assert other == -1
+        return type(self)(self.end_point())
+
+    def __repr__(self):
+        return type(self).__name__ + "(%r)" % (self._start_point,)
+
+
+class ShortEdge(Edge):
+    """
+    A short edge of a doubly truncated simplex.
+    """
+
+    def end_point(self):
+        """
+        The vertex at the end of the edge.
+        """
+        tet, v0, v1, v2 = self._start_point
+        return Vertex(tet, v0, v1, 6 - v0 - v1 - v2)
+
+
+class MiddleEdge(Edge):
+    """
+    A middle edge of a doubly truncated simplex.
+    """
+
+    def end_point(self):
+        """
+        The vertex at the end of the edge.
+        """
+        tet, v0, v1, v2 = self._start_point
+
+        return Vertex(tet, v0, v2, v1)
+
+
+class LongEdge(Edge):
+    """
+    A log edge of a doubly truncated simplex.
+    """
+
+    def end_point(self):
+        """
+        The vertex at the end of the edge.
+        """
+        tet, v0, v1, v2 = self._start_point
+        return Vertex(tet, v1, v0, v2)
+
+
+class Path(tuple):
+    """
+    A tuple of edges that form a path.
+    """
+
+    def __pow__(self, other):
+        """
+        The inverse path can be computes as edge ** -1
+        """
+        assert other == -1
+        return Path([edge ** -1 for edge in self][::-1])
+
+    def __mul__(self, other):
+        """
+        Two paths a, b can be composed as a * b.
+        An edge e can be appended with a * e.
+        """
+
+        if isinstance(other, Path):
+            return Path(self + other)
+        return Path(self + (other,))
+
+
+def _penalty_of_path(path, penalties):
+
+    def penalty(edge):
+        if isinstance(edge, ShortEdge):
+            return penalties[0]
+        if isinstance(edge, MiddleEdge):
+            return penalties[1]
+        return penalties[2]
+
+    return sum([penalty(edge) for edge in path])
+
+
+def _perm4_iterator():
+    for v0 in range(4):
+        for v1 in range(4):
+            if v1 != v0:
+                for v2 in range(4):
+                    if v2 != v0 and v2 != v1:
+                        yield v0, v1, v2, 6 - v0 - v1 - v2
+
+
+def _compute_origin(choose_generators_info):
+    """
+    Using the info from SnapPy's choose_generators_info, return the vertex
+    (0, 1, 2) of the simplex that SnapPy used to compute a spanning tree of
+    the dual 1-skeleton.
+    """
+    # Picks the one tetrahedron with generator_path = -1.
+    # If choose_generators_info comes from a regina triangulation, then
+    # generator_path is missing and we pick the first tetrahedron.
+
+    tet = [info['index'] for info in choose_generators_info
+           if info.get('generator_path', -1) == -1][0]
+    return Vertex(tet, 0, 1, 2)
+
+
+def _compute_point_identification_dict(choose_generators_info):
+    """
+    A vertex in the fundamental domain is an equivalence class of
+    vertices (tet, v0, v1, v2) of doubly truncated simplicies under face
+    gluings not corresponding to generators.
+
+    This method computes the equivalence classes and returns them
+    as dictionary mapping a vertex quadruple (tet, v0, v1, v2) to
+    the set of equivalent triples.
+    """
+
+    # Initialize: each vertex is mapped to set of only itself
+    d = {Vertex(tet, v0, v1, v2): {Vertex(tet, v0, v1, v2)}
+         for tet in range(len(choose_generators_info))
+         for v0, v1, v2, v3 in _perm4_iterator()}
+
+    # Go through all points on faces not corresponding to
+    # generators
+    for this_tet, info in enumerate(choose_generators_info):
+        for this_v0, this_v1, this_v2, this_v3 in _perm4_iterator():
+            if info['generators'][this_v0] == 0:
+
+                # Determine the point
+                this_pt = Vertex(this_tet, this_v1, this_v2, this_v3)
+
+                # And the point identified by the face gluing
+                other_tet = info['neighbors'][this_v0]
+                gluing = info['gluings'][this_v0]
+                other_pt = Vertex(
+                    other_tet,
+                    gluing[this_v1], gluing[this_v2], gluing[this_v3])
+
+                # These two points are in the same equivalence class,
+                # thus merge the two sets corresponding to these points
+                identified_pts = d[this_pt] | d[other_pt]
+
+                # And set that set as new value for each of these points
+                for pt in identified_pts:
+                    d[pt] = identified_pts
+
+    return d
+
+
+def _compute_point_to_shortest_path(point_identification_dict, origin,
+                                    penalties):
+    """
+    Given the equivalence classes of quadruples (tet, v0, v1, v2) representing
+    the same vertex in the fundamental domain and an origin,
+    compute a shortest path from the origin to each vertex.
+
+    This is returned as a dictionary mapping each triple to a shortest path.
+    Triples corresponding to the same identified vertex all have the same
+    path.
+    """
+
+    # Record the paths in d
+    d = {}
+
+    # As said above, equivalent triples map to the same path.
+    # To maintain this, here is a helper that produces a dictionary with
+    # this property. It maps all triples equivalent to pt to path.
+
+    def identified_points_to_path(pt, path):
+        return {
+            identified_pt: path
+              for identified_pt in point_identification_dict[pt] }
+
+    # Trivial paths for points identified with origin
+    previously_added = identified_points_to_path(origin, Path())
+
+    # Iterate to compute longer and longer paths until an iteration
+    # yielded no more paths.
+    while previously_added:
+
+        # First, insert all paths into the dictionary that we computed
+        # in the previous iteration
+        d.update(previously_added)
+
+        # Compute new paths by starting from the paths computed in the
+        # previous iteration
+        new_paths = {}
+
+        # Iterate through the previously added paths
+        # We want the algorithm to be deterministic, thus sort items.
+        for pt, path in sorted(previously_added.items()):
+            # Look at all edges starting where the previous path ended
+            for edge in pt.edges_starting_at_vertex():
+                # Construct a new path by appending the edge and
+                # add that path
+                new_path = path * edge
+                new_end_point = edge.end_point()
+
+                # If the end point of this edge does not have a path
+                # yet or the new path is shorter.
+                if (new_end_point not in d
+                    or _penalty_of_path(new_path, penalties) <
+                               _penalty_of_path(d[new_end_point], penalties)):
+                    new_paths.update(
+                        identified_points_to_path(new_end_point, new_path))
+
+        # We are at the end of the iteration, remember the paths
+        # constructed now for the next iteration.
+        previously_added = new_paths
+
+    return d
+
+
+def _compute_num_generators(choose_generators_info):
+    """
+    Compute the number of generators.
+    """
+
+    return max([ max(info['generators']) for info in choose_generators_info ])
+
+
+def _compute_loops_for_generators_from_info(choose_generators_info,
+                                            point_to_shortest_path,
+                                            penalties):
+    """
+    Using the result of SnapPy's _choose_generators_info() that
+    indicates which face pairings correspond to which generators and
+    the shortest path dictionary computed previously,
+    compute a loop in the short and long edges for each generator.
+    """
+
+    # Allocate an array to hold all the loops
+    num_generators = _compute_num_generators(choose_generators_info)
+    loops_for_generators = num_generators * [ None ]
+
+    # Go through all tets
+    for this_tet, info in enumerate(choose_generators_info):
+        # Go through all faces and vertices on that face
+        for this_v0, this_v1, this_v2, this_v3 in _perm4_iterator():
+            # Consider the face opposite of vertex v0
+            generator_index = info['generators'][this_v0]
+            # If this face corresponds to an outbound_generator
+            if generator_index > 0:
+                # Take the vertex
+                this_pt = Vertex(this_tet, this_v1, this_v2, this_v3)
+
+                # Take the vertex glued to it through face pairing
+                other_tet = info['neighbors'][this_v0]
+                gluing = info['gluings'][this_v0]
+                other_pt = Vertex(
+                    other_tet,
+                    gluing[this_v1], gluing[this_v2], gluing[this_v3])
+
+                # Compute a loop by composing the shortest path to
+                # the vertex with the inverse shortest path to the
+                # glued vertex
+                new_loop = (
+                    point_to_shortest_path[this_pt] *
+                    point_to_shortest_path[other_pt] ** -1 )
+
+                # Save the resulting loop in the array if the array
+                # did not contain a result already or the loop is better
+                # (i.e., has less edges)
+                loop = loops_for_generators[generator_index - 1]
+                if (loop is None
+                    or _penalty_of_path(new_loop, penalties) <
+                                            _penalty_of_path(loop, penalties)):
+                    loops_for_generators[generator_index - 1] = new_loop
+
+    return loops_for_generators
+
+
+def compute_loops_for_generators(M, penalties):
+    """
+    Given a SnapPy Manifold M, return a loop of short, middle, and long edges
+    representing a generator of the fundamental group in the
+    unsimplified presentation for each generator.
+
+    Each short, middle, respectively, long edge has an associate penalty
+    (encoded the triple penalties). For each generator, the method returns
+    a loop with the smallest total penalty.
+    """
+
+    # Get the necessary information from SnapPea kernel
+    M._choose_generators(False, False)
+    choose_generators_info = M._choose_generators_info()
+
+    # Compute which vertices of doubly truncated simplices are identified
+    # to form the fundamental domain
+    point_identification_dict = _compute_point_identification_dict(
+        choose_generators_info)
+
+    # Pick an origin
+    origin = _compute_origin(choose_generators_info)
+
+    # Compute shortest paths form the origin to every vertex
+    point_to_shortest_path = _compute_point_to_shortest_path(
+        point_identification_dict, origin, penalties)
+
+    # Compute the loops
+    return _compute_loops_for_generators_from_info(
+        choose_generators_info, point_to_shortest_path, penalties)
+
+
+def _evaluate_path(coordinate_object, path):
+    """
+    Given PtolemyCoordinates or CrossRatios (or more generally, any object that
+    supports _get_identity_matrix, short_edge, middle_edge, and long_edge) and
+    a path, return the product of the matrices returned by the respective
+    calls to short_edge, middle_edge, and long_edge.
+    """
+
+    # Start with identity
+    m = coordinate_object._get_identity_matrix()
+
+    # Multiply the matrices
+    for edge in path:
+
+        if isinstance(edge, ShortEdge):
+            matrix_method = coordinate_object.short_edge
+        elif isinstance(edge, MiddleEdge):
+            matrix_method = coordinate_object.middle_edge
+        elif isinstance(edge, LongEdge):
+            matrix_method = coordinate_object.long_edge
+        else:
+            raise Exception("Edge of unknown type in path")
+
+        m = matrix.matrix_mult(m, matrix_method(*edge.start_point()))
+
+    return m
+
+
+def images_of_original_generators(coordinate_object, penalties):
+    """
+    Given Ptolemy coordinates or cross ratio (or anything which supports
+    get_manifold and methods to return matrices for short, middle, and long
+    edges) and penalties (triple giving preferences to avoid short, middle,
+    and long edges), give two lists of matrices that are the images and inverse
+    images of the fundamental group generators of the unsimplified presentation.
+    """
+    # Get the manifold
+    M = coordinate_object.get_manifold()
+
+    if M is None:
+        raise Exception("Need to have a manifold")
+
+    loops = compute_loops_for_generators(M, penalties=penalties)
+
+    return (
+        [ _evaluate_path(coordinate_object, loop      ) for loop in loops ],
+        [ _evaluate_path(coordinate_object, loop ** -1) for loop in loops ])
+
+
+def _apply_hom_to_word(word, G):
+    # No G given means nothing is done to the word
+    if G is None:
+        return word
+
+    # G is a SnapPy Fundamental group
+    if hasattr(G, 'generators_in_originals'):
+
+        result = ""
+
+        # Get how each letter translates into the original generators
+        imgs = G.generators_in_originals()
+        for letter in word:
+
+            if letter.isupper():
+                # Upper case letter correspond to inverses
+                # Inverse is formed by swapping case, then reversing string
+                result += imgs[ord(letter) - ord('A')].swapcase()[::-1]
+            else:
+                result += imgs[ord(letter) - ord('a')]
+        return result
+
+    raise Exception("Given argument is not a SnapPy fundamental group")
+
+
+def evaluate_word(identity_matrix, generator_matrices, inverse_matrices,
+                  word, G):
+
+    # Start with the identity matrix
+    m = identity_matrix
+
+    image_of_word = _apply_hom_to_word(word, G)
+
+    # Iterate through word
+    for letter in image_of_word:
+
+        if letter.isupper():
+            # Upper case letters correspond to inverse generators
+            g = inverse_matrices[ord(letter) - ord('A')]
+        else:
+            g = generator_matrices[ord(letter) - ord('a')]
+
+        # Multiply
+        m = matrix.matrix_mult(m, g)
+
+    return m

snappy/ptolemy/geometricRep.py

@@ -0,0 +1,59 @@
+def compute_geometric_solution(M, N=2, numerical=False,
+                               engine=None,
+                               memory_limit=750000000, directory=None,
+                               prefer_rur=False, data_url=False,
+                               verbose=None):
+    """
+    Given a manifold M, compute the exact or numerical solutions to the
+    Ptolemy variety (pass numerical = True for numerical solutions). The additional
+    options are the same as the ones passed to compute_solutions of a PtolemyVariety.
+
+    >>> from snappy.ptolemy.geometricRep import compute_geometric_solutions
+    >>> compute_geometric_solutions(Manifold("m004")) #doctest: +SKIP
+
+    """
+
+    if verbose is None:
+        verbose = (engine == 'retrieve')
+
+    obstruction_class = 'all' if N % 2 == 0 else None
+    varieties = M.ptolemy_variety(N, obstruction_class=obstruction_class)
+
+    if engine == 'retrieve':
+        sols = varieties.retrieve_solutions(numerical=numerical,
+                                           prefer_rur=prefer_rur,
+                                           data_url=data_url,
+                                           verbose=verbose)
+    else:
+        sols = varieties.compute_solutions(engine=engine,
+                                          numerical=numerical,
+                                          memory_limit=memory_limit,
+                                          directory=directory,
+                                          verbose=verbose)
+
+    for sol in sols.flatten(3):
+        if sol.is_geometric():
+            return sol
+
+    return None
+
+
+def retrieve_geometric_solution(M, N=2,
+                                numerical=False,
+                                prefer_rur=False,
+                                data_url=None,
+                                verbose=True):
+    """
+    Given a manifold M, retrieve the exact or numerical solutions to the
+    Ptolemy variety (pass numerical = True for numerical solutions). The additional
+    options are the same as the ones passed to retrieve_solutions of a PtolemyVariety.
+
+    >>> from snappy.ptolemy.geometricRep import retrieve_geometric_solutions
+    >>> retrieve_geometric_solutions(Manifold("m004")) #doctest: +SKIP
+
+    """
+
+    return compute_geometric_solution(M, N, numerical=numerical,
+                                      engine='retrieve',
+                                      prefer_rur=prefer_rur,
+                                      data_url=data_url, verbose=verbose)