snappy 3.2__cp311-cp311-macosx_10_12_x86_64.whl

snappy/len_spec/tile.py

@@ -0,0 +1,275 @@
+from ..tiling.lifted_tetrahedron import LiftedTetrahedron
+from ..tiling.lifted_tetrahedron_set import (LiftedTetrahedronSet,
+                                             get_lifted_tetrahedron_set)
+from ..tiling.iter_utils import merge_iterables
+from ..tiling.hyperboloid_dict import get_hyperboloid_dict
+from ..tiling.dict_based_set import DictBasedSet
+from ..hyperboloid import o13_inverse
+from ..snap.t3mlite import Mcomplex, simplex
+from ..math_basics import correct_min, correct_max, lower # type: ignore
+from ..matrix import make_identity_matrix
+
+from .geometry import (lower_bound_geodesic_length,
+                       lower_bound_distance_r13_point_truncated_tetrahedron)
+
+import heapq
+from typing import List, Sequence
+
+class LengthSpectrumTile:
+    """
+    Represents a translate of the fundamental domain by the given
+    o13_matrix used to tile H^3. A corresponding word in the unsimplified
+    fundamental group is also given.
+
+    Note that we drop the base tile where the o13_matrix is the identity.
+
+    Thus, for every LengthSpectrumTile, the matrix determines a possibly
+    degenerate geodesic. Here degenerate means that the two endpoints
+    coincide (and the geodesic has length zero) since the matrix is parabolic.
+
+    LengthSpectrumTile's are emitted by compute_length_spectrum_tiles with
+    increasing lower_bound_geodesic_length (more precisely, increasing
+    left endpoint if intervals are used). If we are interested only geodesics
+    up to length L, we need to iterate over the tiles emitted by
+    compute_length_sepctrum_tiles until we have tile where
+    lower_bound_geodesic_length is larger than L.
+
+    Note that the length of the geodesic associated to the o13_matrix can
+    actually be shorter than lower_bound_geodesic_length. This can happen
+    since we can have a parabolic matrix or a matrix conjugate to an
+    earlier matrix we have seen encoding a geodesic we already had seen
+    earlier in a different way.
+
+    This class is similar to snappy.tiling.tile.Tile and
+    snappy.tiling.tile._PendingLiftedTetrahedron but specialized to the
+    length spectrum and corresponds to tiling by fundamental domains.
+    """
+
+    def __init__(self,
+                 word : List[int],
+                 o13_matrix,
+                 lower_bound_geodesic_length):
+        self.word = word
+        self.o13_matrix = o13_matrix
+        self.lower_bound_geodesic_length = lower_bound_geodesic_length
+
+        self._key = lower(lower_bound_geodesic_length)
+
+    def __lt__(self, other):
+        """
+        Used so that we can merge streams of tiles with merge_iterables.
+        """
+        return self._key < other._key
+
+def compute_length_spectrum_tiles(mcomplex : Mcomplex
+                                  ) -> Sequence[LengthSpectrumTile]:
+    """
+    Given the result of mcomplex_for_len_spec, provides a stream of tiles
+    suitable to compute the length spectrum.
+
+    More precisely, to know all geodesics up to length L, we need to
+    iterate the stream until we have a tile with
+    tile.lower_bound_geodesic_length > L.
+    """
+
+    # We spawn a separate tiling process for each tetrahedron.
+    # This process will start tiling a ball about the basepoint of
+    # the given tetrahedron and emits a stream of LengthSpectrumTile's
+    # with increasing lower_bound_geodesic_length.
+    #
+    # We need to merge the result of all these streams to find all
+    # geodesics (up to a certain length L).
+    #
+    # However, we might also find duplicates among these streams.
+    # We de-duplicate them here using the visited_dict.
+    #
+    # For more context:
+    # Recall that mcomplex_for_len_spec added a spine to the manifold.
+    # Each geodesic has to intersect that spine somewhere.
+    #
+    # However, the tiling process for one tetrahedron only takes into
+    # account the intersection of the spine with that particular
+    # tetrahedron.
+    #
+    # See _compute_length_spectrum_tiles_for_tetrahedron for more details.
+
+    max_neg_prod_equal, min_neg_prod_distinct = _max_min_prod(mcomplex)
+    visited_dict = DictBasedSet(
+        get_hyperboloid_dict(max_neg_prod_equal,
+                             min_neg_prod_distinct,
+                             mcomplex.verified))
+
+    # Add (non-translated) base point so that we do not emit the base tile
+    # with the identity matrix
+    visited_dict.add(mcomplex.R13_baseTetInCenter)
+
+    for tile in merge_iterables(
+            [ _compute_length_spectrum_tiles_for_tetrahedron(mcomplex, tet)
+              for tet in mcomplex.Tetrahedra ]):
+        if visited_dict.add(tile.o13_matrix * mcomplex.R13_baseTetInCenter):
+            yield tile
+
+def _compute_length_spectrum_tiles_for_tetrahedron(
+        mcomplex, initial_tetrahedron) -> Sequence[LengthSpectrumTile]:
+
+    """
+    Returns a stream of length spectrum tiles. To know all geodesics
+    up to length L that intersect the restriction of the spine to the
+    given tetrahedron, we need to iterate the stream until we have a tile
+    with tile.lower_bound_geodesic_length > L.
+    """
+
+    # We tile H^3 by lifted tetrahedra by covering a larger and larger ball
+    # about the incenter of the initial_tetrahedron.
+    #
+    # If a lifted tetrahedron is a translated copy of the initial_tetrahedron,
+    # we emit a LengthSpectrumTile. The lower_bound_geodesic_length is computed
+    # from the radius of the covered ball using lower_bound_geodesic_length.
+
+    initial_lifted_tetrahedron = LiftedTetrahedron(
+        initial_tetrahedron, make_identity_matrix(ring=mcomplex.RF, n=4))
+
+    # The pending pieces as priority queue - that is, a python list
+    # but we use heapq to access it.
+    pending_lifted_tetrahedra : Sequence[_PendingLiftedTetrahedron] = []
+
+    # Start tiling with the initial_tetrahedron.
+    heapq.heappush(
+        pending_lifted_tetrahedra,
+        _PendingLiftedTetrahedron(
+            [], initial_lifted_tetrahedron, mcomplex.RF(0)))
+
+    max_neg_prod_equal, min_neg_prod_distinct = _max_min_prod(mcomplex)
+
+    # Initialize data structure recording which lifted tetrahedra have
+    # already been visited while tiling H^3.
+    visited_lifted_tetrahedra : LiftedTetrahedronSet = (
+        get_lifted_tetrahedron_set(
+            base_point=mcomplex.R13_baseTetInCenter,
+            canonical_keys_function=None,
+            act_on_base_point_by_inverse=False,
+            max_neg_prod_equal=max_neg_prod_equal,
+            min_neg_prod_distinct=min_neg_prod_distinct,
+            verified=mcomplex.verified))
+
+    while True:
+        pending_lifted_tetrahedron : _PendingLiftedTetrahedron = (
+            heapq.heappop(pending_lifted_tetrahedra))
+
+        tet = pending_lifted_tetrahedron.lifted_tetrahedron.tet
+        m = pending_lifted_tetrahedron.lifted_tetrahedron.o13_matrix
+
+        if tet is initial_tetrahedron:
+            # Emit Tile
+            yield LengthSpectrumTile(
+                pending_lifted_tetrahedron.word,
+                pending_lifted_tetrahedron.lifted_tetrahedron.o13_matrix,
+                lower_bound_geodesic_length(
+                    pending_lifted_tetrahedron.lower_bound_distance,
+                    initial_tetrahedron.inv_spine_cosh))
+
+        # For all faces ...
+        for f, new_tet in tet.Neighbor.items():
+            # ... except the one that was used to reach this lifted tetrahedron
+            if f == pending_lifted_tetrahedron.entry_cell:
+                continue
+
+            entry_face = tet.Gluing[f].image(f)
+
+            # Inverse of tet.O13_matrices[f]
+            new_m = m * new_tet.O13_matrices[entry_face]
+            new_lifted_tetrahedron = LiftedTetrahedron(new_tet, new_m)
+
+            if not visited_lifted_tetrahedra.add(new_lifted_tetrahedron):
+                continue
+
+            # Compute word
+            word = pending_lifted_tetrahedron.word
+            g = new_tet.GeneratorsInfo[entry_face]
+            if g != 0:
+                word = word + [ -g ]
+
+            # We want to compute the distance of the spine_center to the
+            # lifted tetrahedron.
+            # However, it is cheaper to apply the inverse matrix to the
+            # spine center rather than the matrix to the tetrahedron.
+            lifted_spine_center = (
+                o13_inverse(new_m) * initial_tetrahedron.spine_center)
+
+            heapq.heappush(
+                pending_lifted_tetrahedra,
+                _PendingLiftedTetrahedron(
+                    word,
+                    new_lifted_tetrahedron,
+                    lower_bound_distance_r13_point_truncated_tetrahedron(
+                        lifted_spine_center,
+                        new_tet,
+                        mcomplex.verified),
+                    entry_cell=entry_face))
+
+class _PendingLiftedTetrahedron:
+    """
+    A lifted tetrahedron that still needs to be processed to tile
+    together with the face used to reach this tetrahedron.
+
+    The < operator is overloaded so that the piece with the lowest
+    lower_bound will be picked up next by a priority queue.
+
+    If pieces are processed in this order, then the lower_bound of the
+    next piece will actually be a lower bound for the distance between L
+    and the lifted tetrahedron (with other pending pieces for the same
+    lifted tetrahedron having higher values for lower_bound and thus
+    being further down the queue).
+    """
+
+    def __init__(self,
+                 word,
+                 lifted_tetrahedron : LiftedTetrahedron,
+                 lower_bound_distance,
+                 entry_cell : int = simplex.T):
+        self.word = word
+        self.lifted_tetrahedron = lifted_tetrahedron
+        self.lower_bound_distance = lower_bound_distance
+
+        # Either element of simplex.ZeroSubsimplices (if piece was reached
+        # through another piece) or simplex.T (if this pending piece was
+        # used to start tiling).
+        self.entry_cell = entry_cell
+
+        # For convenience, lower_bound is an interval but it is only
+        # the left value of the interval that is relevant and that we
+        # should use: A < B can be False for two intervals even
+        # when A's left value is lower than B's left value.
+        self._key = lower(lower_bound_distance)
+
+    def __lt__(self, other):
+        return self._key < other._key
+
+def _max_min_prod(mcomplex):
+    min_neg_prod_distinct = (mcomplex.baseTetInRadius/2).cosh()
+    if mcomplex.verified:
+        return (min_neg_prod_distinct, min_neg_prod_distinct)
+    else:
+        max_neg_prod_equal = min(
+            min_neg_prod_distinct,
+            1 + _compute_epsilon(mcomplex.RF))
+        return (max_neg_prod_equal, min_neg_prod_distinct)
+
+def _compute_epsilon(RF):
+    p = RF.precision()
+
+    # We try to be a factor of at least 10^6 smaller than
+    # 1/_compute_epsilon_inverse(RF) in hyperboloid_dict.py.
+    #
+    # This factor will even grow larger as the precision increases.
+    #
+    # That way, we will hopefully fail in _equality_predicate
+    # in hyperboloid_dict rather than failing by not hashing together
+    # lifted tetrahedra that should be the same but are not recognised
+    # as such because of numerical error.
+
+    result = RF(1e-5)
+    if p > 53:
+        result *= RF(0.5) ** ((p - 53) / 2)
+
+    return result

snappy/len_spec/word.py

@@ -0,0 +1,86 @@
+from ..SnapPy import reduce_list_word, inverse_list_word
+
+from typing import List
+
+def simplify_geodesic_word(word : List[int]) -> List[int]:
+    """
+    Simplifies given word. It can change the word by a conjugate or
+    invert it.
+
+    More precisely, it cancels pairs of generator and inverse. First if
+    they are next to each other and then if they are at opposite ends of
+    the word. It then cyclically rotates the word and its inverse to take
+    the lexicographically smallest when ordering the generators as
+    1, -1, 2, -2, 3, -3, ...
+
+    >>> simplify_geodesic_word([])
+    []
+    >>> simplify_geodesic_word([1])
+    [1]
+    >>> simplify_geodesic_word([1, 2])
+    [1, 2]
+    >>> simplify_geodesic_word([-1, 2, -2, 1])
+    []
+    >>> simplify_geodesic_word([-1, 3, 2, -2, 1])
+    [3]
+    >>> simplify_geodesic_word([-1, 3, 4, 2, -2, 1])
+    [3, 4]
+    >>> simplify_geodesic_word([-1, 4, 3, 2, -2, 1])
+    [3, 4]
+    >>> simplify_geodesic_word([-1, -3, -4, 5, 2, -2, 1])
+    [3, -5, 4]
+    """
+
+    return (
+        _rotate_and_optionally_invert(
+            _cancel_conjugation(
+                reduce_list_word(word))))
+
+def _cancel_conjugation(word : List[int]) -> List[int]:
+    """
+    Cancels pairs of generator and inverse at opposite ends of
+    given word.
+
+    >>> _cancel_conjugation([])
+    []
+    >>> _cancel_conjugation([1])
+    [1]
+    >>> _cancel_conjugation([1, -1])
+    []
+    >>> _cancel_conjugation([1, 2, -1])
+    [2]
+    >>> _cancel_conjugation([1, 2, 3, -1])
+    [2, 3]
+    """
+    n = len(word)
+    for i in range(n // 2):
+        k = n - i - 1
+        if word[i] != -word[k]:
+            return word[i:k+1]
+    return word[n // 2 : (n + 1) // 2]
+
+def _rotate_and_optionally_invert(word : List[int]) -> List[int]:
+    """
+    Rotate word and its inverse to pick lexicographically smallest when
+    ordering the generators as 1, -1, 2, -2, 3, -3, ...
+
+    >>> _rotate_and_optionally_invert([3, 4, 5])
+    [3, 4, 5]
+    >>> _rotate_and_optionally_invert([4, 5, 3])
+    [3, 4, 5]
+    >>> _rotate_and_optionally_invert([-3])
+    [3]
+    >>> _rotate_and_optionally_invert([5, 3, 4, -3])
+    [3, 4, -3, 5]
+    """
+    n = len(word)
+
+    if n == 0:
+        return word
+
+    return min(
+        (candidates[i:] + candidates[:i]
+         for candidates in [ word, inverse_list_word(word) ]
+         for i in range(len(word))),
+        key=lambda w: [ 2 * l if l > 0 else 2 * -l + 1
+                        for l in w ])

snappy/manifolds/__init__.py

@@ -0,0 +1,3 @@
+# dummy "package" used to set paths for ../SnapPea.py
+
+pass

snappy/math_basics.py

@@ -0,0 +1,176 @@
+from .sage_helper import _within_sage
+from .exceptions import InsufficientPrecisionError
+
+from functools import reduce
+import operator
+
+__all__ = ['prod',
+           'xgcd',
+           'is_RealIntervalFieldElement',
+           'is_ComplexIntervalFieldElement'
+           'is_Interval',
+           'correct_min',
+           'correct_max',
+           'lower']
+
+def is_Interval(x):
+    """
+    Returns True is x is either a real or complex interval as constructed
+    with RealIntervalField or ComplexIntervalField, respectively.
+    """
+    return is_RealIntervalFieldElement(x) or is_ComplexIntervalFieldElement(x)
+
+if _within_sage:
+    from .sage_helper import prod, xgcd
+
+    from sage.rings.real_mpfi import RealIntervalFieldElement
+    from sage.rings.complex_interval import ComplexIntervalFieldElement
+
+    def is_RealIntervalFieldElement(x):
+        return isinstance(x, RealIntervalFieldElement)
+
+    def is_ComplexIntervalFieldElement(x):
+        return isinstance(x, ComplexIntervalFieldElement)
+
+else:
+
+    def prod(L, initial=None):
+        """
+        Product of all elements in L.
+        If L is empty returns initial (if given) or 1.
+        """
+        if initial is not None:
+            return reduce(operator.mul, L, initial)
+        if L:
+            return reduce(operator.mul, L)
+        return 1
+
+    def xgcd(a, b):
+        r"""
+        Returns a triple ``(g,s,t)`` such that `g = s\cdot a+t\cdot b = \gcd(a,b)`.
+
+        >>> xgcd(56, 44)
+        (4, 4, -5)
+        >>> xgcd(5, 7)
+        (1, 3, -2)
+        >>> xgcd(-5, -7)
+        (1, -3, 2)
+        >>> xgcd(5, -7)
+        (1, 3, 2)
+        >>> xgcd(-5, 7)
+        (1, -3, -2)
+        """
+
+        old_r, r = a, b
+        old_s, s = 1, 0
+        old_t, t = 0, 1
+
+        while r != 0:
+            q = old_r // r
+            old_r, r = r, old_r - q * r
+            old_s, s = s, old_s - q * s
+            old_t, t = t, old_t - q * t
+
+        if old_r > 0:
+            return old_r, old_s, old_t
+        return -old_r, -old_s, -old_t
+
+    def is_RealIntervalFieldElement(x):
+        """
+        is_RealIntervalFieldElement returns whether x is a real
+        interval (constructed with RealIntervalField(precision)(value)).
+        """
+
+        # We do not support interval arithmetic outside of SnapPy,
+        # so always return False.
+        return False
+
+    def is_ComplexIntervalFieldElement(x):
+        """
+        is_ComplexIntervalFieldElement returns whether x is a complex
+        interval (constructed with ComplexIntervalField(precision)(value)).
+        """
+
+        # We do not support interval arithmetic outside of SnapPy,
+        # so always return False.
+        return False
+    
+def correct_min(l):
+    """
+    A version of min that works correctly even when l is a list of
+    real intervals.
+
+    This is needed because python's min returns the wrong result
+    for intervals, for example:
+
+        sage: from sage.all import RIF
+        sage: min(RIF(4,5), RIF(3,6)).endpoints()
+        (4.00000000000000, 5.00000000000000)
+
+    when the correct is answer is [3,5].
+
+    The reason is that python's min(x, y) returns either x or y
+    depending on whether y < x. The correct implementation returns
+    the smallest lower and upper bound across all intervals,
+    respectively.
+    """
+    are_intervals = [is_RealIntervalFieldElement(x) for x in l]
+    if any(are_intervals):
+        if not all(are_intervals):
+            raise TypeError(
+                "Trying to compute min of array where some elements are "
+                "intervals and others are not.")
+        # Work-around ticket https://trac.sagemath.org/ticket/33514
+        # That is: SageMath's min/max happily ignores NaNs.
+        #
+        # >>> a = RIF(1)
+        # >>> b = RIF('NaN')
+        # >>> a.min(b)
+        # 1
+        #
+        for x in l:
+            if x.is_NaN():
+                raise ValueError(
+                    "Trying to compute min of array containing NaN interval.")
+        return reduce(lambda x, y: x.min(y), l)
+    else:
+        for x in l:
+            if not x == x:
+                raise ValueError(
+                    "Trying to compute min of array containing NaN.")
+        return min(l)
+
+
+def correct_max(l):
+    """
+    Analogous to correct_min.
+    """
+    are_intervals = [is_RealIntervalFieldElement(x) for x in l]
+    if any(are_intervals):
+        if not all(are_intervals):
+            raise TypeError(
+                "Trying to compute max of array where some elements are "
+                "intervals and others are not.")
+        # Work-around ticket https://trac.sagemath.org/ticket/33514
+        # See above example.
+        for x in l:
+            if x.is_NaN():
+                raise ValueError(
+                    "Trying to compute max of array containing NaN interval.")
+        return reduce(lambda x, y: x.max(y), l)
+    else:
+        for x in l:
+            if not x == x:
+                raise ValueError(
+                    "Trying to compute max of array containing NaN.")
+        return max(l)
+
+def lower(x):
+    if is_RealIntervalFieldElement(x):
+        if x.is_NaN():
+            raise InsufficientPrecisionError(
+                "A NaN was encountered during a verified computation. "
+                "Increasing the precision will probably fix this.")
+        return x.lower()
+    else:
+        return x