r"""
Automorphism groups and canonical labels

This module implements a general algorithm for computing automorphism groups and
canonical labels of objects. The class of objects in question must be some kind
of structure for which an automorphism is a permutation in $S_n$ for some $n$,
which we call here the order of the object. It should be noted that the word
"canonical" in the term canonical label is used loosely. Given an object $X$,
the canonical label $C(X)$ is just an object for which $C(X) = C(Y)$ for any
$Y$ such that $X \cong Y$.

To understand the algorithm better, a few definitions will help. First one
should note that throughout this module, $S_n$ is defined as the set of
permutations of the set $[n] := \{0, 1, ..., n-1\}$. One speaks of
ordered partitions $\Pi = (C_1, ..., C_k)$ of $[n]$. The $C_i$ are disjoint
subsets of $[n]$ whose union is equal to $[n]$, and we call them cells. A
partition $\Pi_1$ is said to be finer than another partition $\Pi_2$ if every
cell of $\Pi_1$ is a subset of some cell of $\Pi_2$ (in this situation we also
say that $\Pi_2$ is coarser than $\Pi_1$). A partition stack
$\nu = (\Pi_0, ..., \Pi_k)$ is a sequence of partitions such that $\Pi_i$ is
finer than $\Pi_{i-1}$ for each $i$ such that $1 \leq i \leq k$. Sometimes these
are called nested partitions. The depth of $\nu$ is defined to be $k$ and the
degree of $\nu$ is defined to be $n$. Partition stacks are implemented as
\code{PartitionStack} (see automorphism_group_canonical_label.pxd for more
information). Finally, we say that a permutation respects the partition $\Pi$ if
its orbits form a partition which is finer than $\Pi$.

In order to take advantage of the algorithms in this module for a specific kind
of object, one must implement (in Cython) three functions which will be specific
to the kind of objects in question. Pointers to these functions are passed to
the main function of the module, which is \code{get_aut_gp_and_can_lab}. For
specific examples of implementations of these functions, see any of the files in
\code{sage.groups.perm_gps.partn_ref} beginning with "refinement." They are:

A. \code{refine_and_return_invariant}:

    Signature:

    \code{int refine_and_return_invariant(PartitionStack *PS, void *S, int *cells_to_refine_by, int ctrb_len)}

    This function should split up cells in the partition at the top of the
    partition stack in such a way that any automorphism that respects the
    partition also respects the resulting partition. The array
    cells_to_refine_by is a list of the beginning positions of some cells which
    have been changed since the last refinement, of length ctrb_len. It is not
    necessary to use this in an implementation of this function, but it will
    affect performance. One should consult \code{refinement_graphs} for more
    details and ideas for particular implementations.

    Output:

    An integer $I$ invariant under the orbits of $S_n$.  That is, if
    $\gamma \in S_n$, then
    $$ I(G, PS, cells_to_refine_by) = I( \gamma(G), \gamma(PS), \gamma(cells_to_refine_by) ) .$$


B. \code{compare_structures}:

    Signature:

    \code{int compare_structures(int *gamma_1, int *gamma_2, void *S1, void *S2, int degree)}

    This function must implement a total ordering on the set of objects of fixed
    order. Return:
        -1 if \code{gamma_1^{-1}(S1) < gamma_2^{-1}(S2)},
        0 if \code{gamma_1^{-1}(S1) == gamma_2^{-1}(S2)},
        1 if \code{gamma_1^{-1}(S1) > gamma_2^{-1}(S2)}.

    The value ``degree`` indicates the degree of the permutations ``gamma1`` and
    ``gamma_2``.

    Important note:

    The permutations are thought of as being input in inverse form, and this can
    lead to subtle bugs. One is encouraged to consult existing implementations
    to make sure the right thing is being done: this is so that you can avoid
    *actually* needing to compute the inverse.

C. \code{all_children_are_equivalent}:

    Signature:

    \code{bint all_children_are_equivalent(PartitionStack *PS, void *S)}

    This function must return False unless it is the case that each discrete
    partition finer than the top of the partition stack is equivalent to the
    others under some automorphism of S. The converse need not hold: if this is
    indeed the case, it still may return False. This function is originally used
    as a consequence of Lemma 2.25 in [1].

EXAMPLES::

    sage: import sage.groups.perm_gps.partn_ref.automorphism_group_canonical_label

REFERENCE:

- [1] McKay, Brendan D. Practical Graph Isomorphism. Congressus Numerantium,
  Vol. 30 (1981), pp. 45-87.

"""

#*****************************************************************************
#       Copyright (C) 2006 - 2011 Robert L. Miller <rlmillster@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#                  http://www.gnu.org/licenses/
#*****************************************************************************

from __future__ import print_function

from libc.string cimport memcmp, memcpy
from cysignals.memory cimport sig_malloc, sig_realloc, sig_free

from .data_structures cimport *
include "sage/data_structures/bitset.pxi"

cdef inline int agcl_cmp(int a, int b):
    if a < b: return -1
    elif a == b: return 0
    else: return 1

# Functions

cdef bint all_children_are_equivalent_trivial(PartitionStack *PS, void *S):
    return 0

cdef int refine_and_return_invariant_trivial(PartitionStack *PS, void *S, int *cells_to_refine_by, int ctrb_len):
    return 0

cdef int compare_structures_trivial(int *gamma_1, int *gamma_2, void *S1, void *S2, int degree):
    return 0

def test_get_aut_gp_and_can_lab_trivially(int n=6,
    list partition=[[0,1,2],[3,4],[5]], canonical_label=True, base=False):
    """
    sage: tttt = sage.groups.perm_gps.partn_ref.automorphism_group_canonical_label.test_get_aut_gp_and_can_lab_trivially
    sage: tttt()
    12
    sage: tttt(canonical_label=False, base=False)
    12
    sage: tttt(canonical_label=False, base=True)
    12
    sage: tttt(canonical_label=True, base=True)
    12
    sage: tttt(n=0, partition=[])
    1
    sage: tttt(n=0, partition=[], canonical_label=False, base=False)
    1
    sage: tttt(n=0, partition=[], canonical_label=False, base=True)
    1
    sage: tttt(n=0, partition=[], canonical_label=True, base=True)
    1

    """
    cdef aut_gp_and_can_lab *output
    cdef Integer I = Integer(0)
    cdef PartitionStack *part
    part = PS_from_list(partition)
    if part is NULL:
        raise MemoryError
    cdef object empty_list = []
    output = get_aut_gp_and_can_lab(<void *> empty_list, part, n, &all_children_are_equivalent_trivial, &refine_and_return_invariant_trivial, &compare_structures_trivial, canonical_label, NULL, NULL, NULL)
    SC_order(output.group, 0, I.value)
    print(I)
    PS_dealloc(part)
    deallocate_agcl_output(output)

def test_intersect_parabolic_with_alternating(int n=9, list partition=[[0,1,2],[3,4],[5,6,7,8]]):
    """
    A test for nontrivial input group in computing automorphism groups.

    TESTS::

        sage: from sage.groups.perm_gps.partn_ref.automorphism_group_canonical_label import test_intersect_parabolic_with_alternating as tipwa
        sage: tipwa()
        144
        sage: tipwa(5, [[0],[1],[2],[3,4]])
        1
        sage: tipwa(5, [[0],[1],[2,3,4]])
        3
        sage: tipwa(5, [[0,1],[2,3,4]])
        6
        sage: tipwa(7, [[0,1,2,3,4,5,6]])
        2520
        sage: factorial(7)/2
        2520
        sage: tipwa(9, [[0,1,2,3],[4,5,6,7,8]])
        1440

    """
    cdef aut_gp_and_can_lab *output
    cdef Integer I = Integer(0)
    cdef PartitionStack *part
    part = PS_from_list(partition)
    if part is NULL:
        raise MemoryError
    cdef StabilizerChain *group = SC_alternating_group(part.degree)
    if group is NULL:
        PS_dealloc(part)
        raise MemoryError
    cdef object empty_list = []
    output = get_aut_gp_and_can_lab(<void *> empty_list, part, n, &all_children_are_equivalent_trivial, &refine_and_return_invariant_trivial, &compare_structures_trivial, 0, group, NULL, NULL)
    SC_order(output.group, 0, I.value)
    print(I)
    PS_dealloc(part)
    SC_dealloc(group)
    deallocate_agcl_output(output)

cdef int compare_perms(int *gamma_1, int *gamma_2, void *S1, void *S2, int degree):
    cdef list MS1 = <list> S1
    cdef list MS2 = <list> S2
    cdef int i, j
    for i from 0 <= i < degree:
        j = agcl_cmp(MS1[gamma_1[i]], MS2[gamma_2[i]])
        if j != 0: return j
    return 0

def coset_rep(list perm=[0,1,2,3,4,5], list gens=[[1,2,3,4,5,0]]):
    """
    Given a group G generated by the given generators, defines a map from the
    Symmetric group to G so that any two elements from the same right coset go
    to the same element. Tests nontrivial input group when computing canonical
    labels.

    TESTS::

        sage: from sage.groups.perm_gps.partn_ref.automorphism_group_canonical_label import coset_rep
        sage: coset_rep()
        [5, 0, 1, 2, 3, 4]
        sage: gens = [[1,2,3,0]]
        sage: reps = []
        sage: for p in SymmetricGroup(4):
        ....:   p = [p(i)-1 for i in range(1,5)]
        ....:   r = coset_rep(p, gens)
        ....:   if r not in reps:
        ....:       reps.append(r)
        sage: len(reps)
        6
        sage: gens = [[1,0,2,3],[0,1,3,2]]
        sage: reps = []
        sage: for p in SymmetricGroup(4):
        ....:   p = [p(i)-1 for i in range(1,5)]
        ....:   r = coset_rep(p, gens)
        ....:   if r not in reps:
        ....:       reps.append(r)
        sage: len(reps)
        6
        sage: gens = [[1,2,0,3]]
        sage: reps = []
        sage: for p in SymmetricGroup(4):
        ....:   p = [p(i)-1 for i in range(1,5)]
        ....:   r = coset_rep(p, gens)
        ....:   if r not in reps:
        ....:       reps.append(r)
        sage: len(reps)
        8

    """
    cdef int i, n = len(perm)
    assert all(len(g) == n for g in gens)
    cdef aut_gp_and_can_lab *output
    cdef Integer I = Integer(0)
    cdef PartitionStack *part
    part = PS_new(n, 1)
    cdef int *c_perm = <int *> sig_malloc(n * sizeof(int))
    cdef StabilizerChain *group = SC_new(n, 1)
    if part is NULL or c_perm is NULL or group is NULL:
        sig_free(c_perm)
        PS_dealloc(part)
        SC_dealloc(group)
        raise MemoryError
    for g in gens:
        for i from 0 <= i < n:
            c_perm[i] = g[i]
        SC_insert(group, 0, c_perm, 1)
    output = get_aut_gp_and_can_lab(<void *> perm, part, n, &all_children_are_equivalent_trivial, &refine_and_return_invariant_trivial, &compare_perms, 1, group, NULL, NULL)
    SC_order(output.group, 0, I.value)
    assert I == 1
    r_inv = list(xrange(n))
    for i from 0 <= i < n:
        r_inv[output.relabeling[i]] = i
    label = [perm[r_inv[i]] for i in range(n)]
    PS_dealloc(part)
    SC_dealloc(group)
    deallocate_agcl_output(output)
    sig_free(c_perm)
    return label

cdef aut_gp_and_can_lab *allocate_agcl_output(int n):
    r"""
    Allocate an instance of the aut_gp_and_can_lab struct of degree n. This can
    be input to the get_aut_gp_and_can_lab function, and the output will be
    stored to it.
    """
    cdef aut_gp_and_can_lab *output = <aut_gp_and_can_lab *> sig_malloc(sizeof(aut_gp_and_can_lab))
    if output is NULL:
        return NULL
    output.group = SC_new(n)
    output.relabeling = <int *> sig_malloc(n*sizeof(int))
    output.generators = <int *> sig_malloc(2*n*n*sizeof(int))
    output.size_of_generator_array = 2*n*n
    if output.group      is NULL or \
       output.relabeling is NULL or \
       output.generators is NULL:
        deallocate_agcl_output(output)
        return NULL
    return output

cdef void deallocate_agcl_output(aut_gp_and_can_lab *output):
    r"""
    Deallocates an aut_gp_and_can_lab struct.
    """
    if output is not NULL:
        SC_dealloc(output.group)
        sig_free(output.relabeling)
        sig_free(output.generators)
    sig_free(output)

cdef agcl_work_space *allocate_agcl_work_space(int n):
    r"""
    Allocates work space for the get_aut_gp_and_can_lab function. It can be
    input to the function in which case it must be deallocated after the
    function is called.
    """
    cdef int *int_array

    cdef agcl_work_space *work_space
    work_space = <agcl_work_space *> sig_malloc(sizeof(agcl_work_space))
    if work_space is NULL:
        return NULL

    work_space.degree = n
    int_array = <int *> sig_malloc((n*n + # for perm_stack
                                     n   + # for label_indicators
                                     7*n   # for int_array
                                    )*sizeof(int))
    work_space.group1 = SC_new(n)
    work_space.group2 = SC_new(n)
    work_space.label_ps = PS_new(n,0)
    work_space.bitset_array = <bitset_t *> sig_malloc((n + 2*len_of_fp_and_mcr + 1)*sizeof(bitset_t))
    work_space.orbits_of_subgroup = OP_new(n)
    work_space.orbits_of_permutation = OP_new(n)
    work_space.first_ps = PS_new(n,0)

    if int_array                        is NULL or \
       work_space.group1                is NULL or \
       work_space.group2                is NULL or \
       work_space.label_ps              is NULL or \
       work_space.bitset_array          is NULL or \
       work_space.orbits_of_subgroup    is NULL or \
       work_space.orbits_of_permutation is NULL or \
       work_space.first_ps              is NULL:
        deallocate_agcl_work_space(work_space)
        return NULL

    work_space.perm_stack       = int_array
    work_space.label_indicators = int_array + n*n
    work_space.int_array        = int_array + n*n + n

    cdef int i
    for i from 0 <= i < n + 2*len_of_fp_and_mcr + 1:
        work_space.bitset_array[i].bits = NULL
    try:
        for i from 0 <= i < n + 2*len_of_fp_and_mcr + 1:
            bitset_init(work_space.bitset_array[i], n)
    except MemoryError:
        deallocate_agcl_work_space(work_space)
        return NULL
    return work_space

cdef void deallocate_agcl_work_space(agcl_work_space *work_space):
    r"""
    Deallocate work space for the get_aut_gp_and_can_lab function.
    """
    if work_space is NULL:
        return
    cdef int i, n = work_space.degree
    if work_space.bitset_array is not NULL:
        for i from 0 <= i < n + 2*len_of_fp_and_mcr + 1:
            bitset_free(work_space.bitset_array[i])
    sig_free(work_space.perm_stack)
    SC_dealloc(work_space.group1)
    SC_dealloc(work_space.group2)
    PS_dealloc(work_space.label_ps)
    sig_free(work_space.bitset_array)
    OP_dealloc(work_space.orbits_of_subgroup)
    OP_dealloc(work_space.orbits_of_permutation)
    PS_dealloc(work_space.first_ps)
    sig_free(work_space)

cdef aut_gp_and_can_lab *get_aut_gp_and_can_lab(void *S,
    PartitionStack *partition, int n,
    bint (*all_children_are_equivalent)(PartitionStack *PS, void *S),
    int (*refine_and_return_invariant)\
         (PartitionStack *PS, void *S, int *cells_to_refine_by, int ctrb_len),
    int (*compare_structures)(int *gamma_1, int *gamma_2, void *S1, void *S2, int degree),
    bint canonical_label, StabilizerChain *input_group,
    agcl_work_space *work_space_prealloc, aut_gp_and_can_lab *output_prealloc) except NULL:
    """
    Traverse the search space for subgroup/canonical label calculation.

    INPUT:
    S -- pointer to the structure
    partition -- PartitionStack representing a partition of the points
    len_partition -- length of the partition
    n -- the number of points (points are assumed to be 0,1,...,n-1)
    canonical_label -- whether to search for canonical label - if True, return
        the permutation taking S to its canonical label
    all_children_are_equivalent -- pointer to a function
        INPUT:
        PS -- pointer to a partition stack
        S -- pointer to the structure
        OUTPUT:
        bint -- returns True if it can be determined that all refinements below
            the current one will result in an equivalent discrete partition
    refine_and_return_invariant -- pointer to a function
        INPUT:
        PS -- pointer to a partition stack
        S -- pointer to the structure
        alpha -- an array consisting of numbers, which indicate the starting
            positions of the cells to refine against (will likely be modified)
        OUTPUT:
        int -- returns an invariant under application of arbitrary permutations
    compare_structures -- pointer to a function
        INPUT:
        gamma_1, gamma_2 -- (list) permutations of the points of S1 and S2
        S1, S2 -- pointers to the structures
        degree -- degree of gamma_1 and 2
        OUTPUT:
        int -- 0 if gamma_1(S1) = gamma_2(S2), otherwise -1 or 1 (see docs for cmp),
            such that the set of all structures is well-ordered

    NOTE:
    The partition ``partition1`` *must* satisfy the property that in each cell,
    the smallest element occurs first!

    OUTPUT:
    pointer to a aut_gp_and_can_lab struct

    """
    cdef PartitionStack *current_ps
    cdef PartitionStack *first_ps
    cdef PartitionStack *label_ps
    cdef int first_meets_current = -1
    cdef int label_meets_current
    cdef int current_kids_are_same = 1
    cdef int first_kids_are_same

    cdef int *current_indicators
    cdef int *first_indicators
    cdef int *label_indicators
    cdef int first_and_current_indicator_same
    cdef int label_and_current_indicator_same = -1
    cdef int compared_current_and_label_indicators

    cdef OrbitPartition *orbits_of_subgroup
    cdef OrbitPartition *orbits_of_permutation
    cdef OrbitPartition *orbits_of_supergroup
    cdef int subgroup_primary_orbit_size = 0
    cdef int minimal_in_primary_orbit

    cdef bitset_t *fixed_points_of_generators # i.e. fp
    cdef bitset_t *minimal_cell_reps_of_generators # i.e. mcr
    cdef int index_in_fp_and_mcr = -1

    cdef bitset_t *vertices_to_split
    cdef bitset_t *vertices_have_been_reduced
    cdef int *permutation
    cdef int *label_perm
    cdef int *id_perm
    cdef int *cells_to_refine_by
    cdef int *vertices_determining_current_stack
    cdef int *perm_stack
    cdef StabilizerChain *group = NULL
    cdef StabilizerChain *old_group
    cdef StabilizerChain *tmp_gp

    cdef int i, j, k, ell, b
    cdef bint discrete, automorphism, update_label
    cdef bint backtrack, new_vertex, narrow, mem_err = 0

    cdef aut_gp_and_can_lab *output
    cdef agcl_work_space *work_space

    if output_prealloc is not NULL:
        output = output_prealloc
        output.group.base_size = 0
    else:
        output = allocate_agcl_output(n)
        if output is NULL:
            raise MemoryError

    output.num_gens = 0
    if n == 0:
        return output

    if work_space_prealloc is not NULL:
        work_space = work_space_prealloc
    else:
        work_space = allocate_agcl_work_space(n)
        if work_space is NULL:
            if output_prealloc is NULL:
                deallocate_agcl_output(output)
            raise MemoryError

    # Allocate:
    if input_group is not NULL:
        perm_stack                     = work_space.perm_stack
        group                          = work_space.group1
        old_group                      = work_space.group2
        orbits_of_supergroup           = input_group.OP_scratch
        SC_copy_nomalloc(group, input_group, n)
        SC_identify(perm_stack, n)
    if canonical_label:
        label_indicators               = work_space.label_indicators
        label_ps                       = work_space.label_ps
    first_ps                           = work_space.first_ps
    orbits_of_subgroup                 = work_space.orbits_of_subgroup
    orbits_of_permutation              = work_space.orbits_of_permutation

    current_indicators                 = work_space.int_array
    first_indicators                   = work_space.int_array +   n
    permutation                        = work_space.int_array + 2*n
    id_perm                            = work_space.int_array + 3*n
    cells_to_refine_by                 = work_space.int_array + 4*n
    vertices_determining_current_stack = work_space.int_array + 5*n
    label_perm                         = work_space.int_array + 6*n

    fixed_points_of_generators         = work_space.bitset_array
    minimal_cell_reps_of_generators    = work_space.bitset_array + len_of_fp_and_mcr
    vertices_to_split                  = work_space.bitset_array + 2*len_of_fp_and_mcr
    vertices_have_been_reduced         = work_space.bitset_array + 2*len_of_fp_and_mcr + n

    if work_space_prealloc is not NULL:
        OP_clear(orbits_of_subgroup)

    bitset_zero(vertices_have_been_reduced[0])
    current_ps = partition
    current_ps.depth = 0

    # default values of "infinity"
    for i from 0 <= i < n:
        first_indicators[i] = -1
    if canonical_label:
        for i from 0 <= i < n:
            label_indicators[i] = -1

    # set up the identity permutation
    for i from 0 <= i < n:
        id_perm[i] = i

    # Our first refinement needs to check every cell of the partition,
    # so cells_to_refine_by needs to be a list of pointers to each cell.
    j = 1
    cells_to_refine_by[0] = 0
    for i from 0 < i < n:
        if current_ps.levels[i-1] == 0:
            cells_to_refine_by[j] = i
            j += 1
    # Ignore the invariant this time, since we are
    # creating the root of the search tree.
    if input_group is NULL:
        refine_and_return_invariant(current_ps, S, cells_to_refine_by, j)
    else:
        refine_also_by_orbits(current_ps, S, refine_and_return_invariant,
            cells_to_refine_by, j, group, perm_stack)
    PS_move_all_mins_to_front(current_ps)

    # Refine down to a discrete partition
    while not PS_is_discrete(current_ps):
        i = current_ps.depth
        if not all_children_are_equivalent(current_ps, S):
            current_kids_are_same = i + 1
        vertices_determining_current_stack[i] = PS_first_smallest(current_ps, vertices_to_split[i])
        bitset_unset(vertices_have_been_reduced[0], i)
        if input_group is not NULL:
            OP_clear(orbits_of_supergroup)
            for j from i <= j < group.base_size:
                for ell from 0 <= ell < group.num_gens[j]:
                    OP_merge_list_perm(orbits_of_supergroup, group.generators[j] + n*ell)
            b = orbits_of_supergroup.mcr[OP_find(orbits_of_supergroup, perm_stack[i*n + vertices_determining_current_stack[i]])]
            tmp_gp = group
            group = old_group
            old_group = tmp_gp
            if SC_insert_base_point_nomalloc(group, old_group, i, b):
                mem_err = 1
                break
            current_indicators[i] = split_point_and_refine_by_orbits(current_ps,
                vertices_determining_current_stack[i], S, refine_and_return_invariant,
                cells_to_refine_by, group, perm_stack)
        else:
            current_indicators[i] = split_point_and_refine(current_ps, vertices_determining_current_stack[i], S, refine_and_return_invariant, cells_to_refine_by)
        PS_move_all_mins_to_front(current_ps)
        first_indicators[i] = current_indicators[i]
        if canonical_label:
            label_indicators[i] = current_indicators[i]
        SC_add_base_point(output.group, vertices_determining_current_stack[i])

    if not mem_err:
        first_meets_current = current_ps.depth
        first_kids_are_same = current_ps.depth
        first_and_current_indicator_same = current_ps.depth
        PS_copy_from_to(current_ps, first_ps)
        if canonical_label:
            label_meets_current = current_ps.depth
            label_and_current_indicator_same = current_ps.depth
            compared_current_and_label_indicators = 0
            PS_copy_from_to(current_ps, label_ps)
            if input_group is not NULL:
                if compute_relabeling(group, old_group, label_ps.entries, label_perm):
                    mem_err = 1
        current_ps.depth -= 1

    # Main loop:
    while current_ps.depth != -1:

        if mem_err:
            if output_prealloc is NULL:
                deallocate_agcl_output(output)
            if work_space_prealloc is NULL:
                deallocate_agcl_work_space(work_space_prealloc)
            raise MemoryError

        # If necessary, update label_meets_current
        if canonical_label and label_meets_current > current_ps.depth:
            label_meets_current = current_ps.depth

        # I. Search for a new vertex to split, and update subgroup information
        new_vertex = 0
        if current_ps.depth > first_meets_current:
            # If we are not at a node of the first stack, reduce size of
            # vertices_to_split by using the symmetries we already know.
            if not bitset_check(vertices_have_been_reduced[0], current_ps.depth):
                for i from 0 <= i <= index_in_fp_and_mcr:
                    j = 0
                    while j < current_ps.depth and bitset_check(fixed_points_of_generators[i], vertices_determining_current_stack[j]):
                        j += 1
                    # If each vertex split so far is fixed by generator i,
                    # then remove elements of vertices_to_split which are
                    # not minimal in their orbits under generator i.
                    if j == current_ps.depth:
                        for k from 0 <= k < n:
                            if bitset_check(vertices_to_split[current_ps.depth], k) and not bitset_check(minimal_cell_reps_of_generators[i], k):
                                bitset_flip(vertices_to_split[current_ps.depth], k)
                bitset_flip(vertices_have_been_reduced[0], current_ps.depth)
            # Look for a new point to split.
            i = vertices_determining_current_stack[current_ps.depth] + 1
            i = bitset_next(vertices_to_split[current_ps.depth], i)
            if i != -1:
                # There is a new point.
                vertices_determining_current_stack[current_ps.depth] = i
                new_vertex = 1
            else:
                # No new point: backtrack.
                current_ps.depth -= 1
        else:
            # If we are at a node of the first stack, the above reduction
            # will not help. Also, we must update information about
            # primary orbits here.
            if current_ps.depth < first_meets_current:
                # If we are done searching under this part of the first
                # stack, then first_meets_current is one higher, and we
                # are looking at a new primary orbit (corresponding to a
                # larger subgroup in the stabilizer chain).
                first_meets_current = current_ps.depth
                minimal_in_primary_orbit = output.group.base_orbits[current_ps.depth][0]
            while True:
                i = vertices_determining_current_stack[current_ps.depth]
                # This was the last point to be split here.
                # If it has been added to the primary orbit, update size info.
                if output.group.parents[current_ps.depth][i] != -1:
                    subgroup_primary_orbit_size += 1
                # Look for a new point to split.
                i += 1
                i = bitset_next(vertices_to_split[current_ps.depth], i)
                if i != -1:
                    # There is a new point.
                    vertices_determining_current_stack[current_ps.depth] = i
                    if orbits_of_subgroup.mcr[OP_find(orbits_of_subgroup, i)] == i:
                        new_vertex = 1
                        break
                else:
                    # No new point: backtrack.
                    # Note that now, we are backtracking up the first stack.
                    vertices_determining_current_stack[current_ps.depth] = -1
                    # If every choice of point to split gave something in the
                    # (same!) primary orbit, then all children of the first
                    # stack at this point are equivalent.
                    j = 0
                    for i from 0 <= i < n:
                        if bitset_check(vertices_to_split[current_ps.depth], i):
                            j += 1
                    if j == subgroup_primary_orbit_size and first_kids_are_same == current_ps.depth+1:
                        first_kids_are_same = current_ps.depth
                    subgroup_primary_orbit_size = 0
                    current_ps.depth -= 1
                    break
        if not new_vertex:
            continue

        if current_kids_are_same > current_ps.depth + 1:
            current_kids_are_same = current_ps.depth + 1
        if first_and_current_indicator_same > current_ps.depth:
            first_and_current_indicator_same = current_ps.depth
        if canonical_label and label_and_current_indicator_same >= current_ps.depth:
            label_and_current_indicator_same = current_ps.depth
            compared_current_and_label_indicators = 0

        # II. Refine down to a discrete partition, or until
        # we leave the part of the tree we are interested in
        discrete = 0
        backtrack = 0
        while True:
            i = current_ps.depth
            if input_group is not NULL:
                current_indicators[i] = split_point_and_refine_by_orbits(current_ps,
                    vertices_determining_current_stack[i], S,
                    refine_and_return_invariant, cells_to_refine_by,
                    group, perm_stack)
            else:
                current_indicators[i] = split_point_and_refine(current_ps,
                    vertices_determining_current_stack[i], S,
                    refine_and_return_invariant, cells_to_refine_by)
            PS_move_all_mins_to_front(current_ps)
            if first_and_current_indicator_same == i and \
              current_indicators[i] == first_indicators[i] and \
              stacks_are_equivalent(first_ps, current_ps):
                first_and_current_indicator_same += 1
            if canonical_label:
                if compared_current_and_label_indicators == 0:
                    if label_indicators[i] == -1:
                        compared_current_and_label_indicators = -1
                    else:
                        compared_current_and_label_indicators = agcl_cmp(current_indicators[i], label_indicators[i])
                if label_and_current_indicator_same == i and compared_current_and_label_indicators == 0:
                    label_and_current_indicator_same += 1
                if compared_current_and_label_indicators > 0:
                    label_indicators[i] = current_indicators[i]
            if first_and_current_indicator_same < current_ps.depth and (not canonical_label or compared_current_and_label_indicators < 0):
                backtrack = 1
                break
            if PS_is_discrete(current_ps):
                discrete = 1
                break
            vertices_determining_current_stack[current_ps.depth] = PS_first_smallest(current_ps, vertices_to_split[current_ps.depth])
            if input_group is not NULL:
                i = current_ps.depth
                k = vertices_determining_current_stack[i]
                if group.parents[i][perm_stack[n*i + k]] == -1:
                    # if we get here then canonical_label must be true
                    # and we have to make a change of base
                    OP_clear(orbits_of_supergroup)
                    for j from i <= j < group.base_size:
                        for ell from 0 <= ell < group.num_gens[j]:
                            OP_merge_list_perm(orbits_of_supergroup, group.generators[j] + n*ell)
                    b = orbits_of_supergroup.mcr[OP_find(orbits_of_supergroup, perm_stack[i*n + k])]
                    tmp_gp = group
                    group = old_group
                    old_group = tmp_gp
                    if SC_insert_base_point_nomalloc(group, old_group, i, b):
                        mem_err = 1
                        break
            bitset_unset(vertices_have_been_reduced[0], current_ps.depth)
            if not all_children_are_equivalent(current_ps, S):
                current_kids_are_same = current_ps.depth + 1

        # III. Check for automorphisms and labels
        automorphism = 0
        if discrete:
            if current_ps.depth == first_and_current_indicator_same:
                PS_get_perm_from(current_ps, first_ps, permutation)
                if compare_structures(permutation, id_perm, S, S, n) == 0:
                    if input_group is NULL or SC_contains(group, 0, permutation, 0):
                        # TODO: might be slight optimization for containment using perm_stack
                        automorphism = 1
        if not automorphism:
            if (not canonical_label) or (compared_current_and_label_indicators < 0):
                backtrack = 1
            else:
                # if we get here, discrete must be true
                update_label = 0
                if (compared_current_and_label_indicators > 0) or (current_ps.depth < label_ps.depth):
                    if input_group is not NULL:
                        if compute_relabeling(group, old_group, current_ps.entries, permutation):
                            mem_err = 1
                            break
                    update_label = 1
                else:
                    if input_group is NULL:
                        i = compare_structures(current_ps.entries, label_ps.entries, S, S, n)
                    else:
                        if compute_relabeling(group, old_group, current_ps.entries, permutation):
                            mem_err = 1
                            break
                        i = compare_structures(permutation, label_perm, S, S, n)
                    if i > 0:
                        update_label = 1
                    elif i < 0:
                        backtrack = 1
                    else:
                        if input_group is NULL:
                            PS_get_perm_from(current_ps, label_ps, permutation)
                            automorphism = 1
                        elif memcmp(permutation, label_perm, n*sizeof(int)):
                            SC_invert_perm(group.perm_scratch, permutation, n)
                            SC_mult_perms(permutation, group.perm_scratch, label_perm, n)
                            automorphism = 1
                        else:
                            backtrack = 1
                if update_label:
                    PS_copy_from_to(current_ps, label_ps)
                    if input_group is not NULL:
                        memcpy(label_perm, permutation, n*sizeof(int))
                    compared_current_and_label_indicators = 0
                    label_meets_current = current_ps.depth
                    label_and_current_indicator_same = current_ps.depth
                    label_indicators[current_ps.depth] = -1
                    backtrack = 1
        if automorphism:
            if index_in_fp_and_mcr < len_of_fp_and_mcr - 1:
                index_in_fp_and_mcr += 1
            bitset_zero(fixed_points_of_generators[index_in_fp_and_mcr])
            bitset_zero(minimal_cell_reps_of_generators[index_in_fp_and_mcr])
            OP_clear(orbits_of_permutation)
            for i from 0 <= i < n:
                OP_join(orbits_of_permutation, i, permutation[i])
            bitset_zero(minimal_cell_reps_of_generators[index_in_fp_and_mcr])
            for i from 0 <= i < n:
                if permutation[i] == i:
                    bitset_set(fixed_points_of_generators[index_in_fp_and_mcr], i)
                    bitset_set(minimal_cell_reps_of_generators[index_in_fp_and_mcr], i)
                else:
                    bitset_unset(fixed_points_of_generators[index_in_fp_and_mcr], i)
                    if orbits_of_permutation.parent[i] == i:
                        bitset_set(minimal_cell_reps_of_generators[index_in_fp_and_mcr], orbits_of_permutation.mcr[i])
            if OP_merge_list_perm(orbits_of_subgroup, permutation): # if permutation made orbits coarser
                # add permutation as a generator of the automorphism group
                if n*output.num_gens == output.size_of_generator_array:
                    # must double its size
                    output.size_of_generator_array *= 2
                    output.generators = <int *> sig_realloc( output.generators, output.size_of_generator_array * sizeof(int) )
                    if output.generators is NULL:
                        mem_err = True
                        continue # main loop
                j = n*output.num_gens
                for i from 0 <= i < n:
                    output.generators[j + i] = permutation[i]
                output.num_gens += 1
                if SC_update_tree(output.group, first_meets_current, permutation, 1):
                    mem_err = 1
                    continue # main loop
                if orbits_of_subgroup.mcr[OP_find(orbits_of_subgroup, minimal_in_primary_orbit)] != minimal_in_primary_orbit:
                    current_ps.depth = first_meets_current
                    continue # main loop
            if canonical_label:
                current_ps.depth = label_meets_current
            else:
                current_ps.depth = first_meets_current
            if bitset_check(vertices_have_been_reduced[0], current_ps.depth):
                bitset_and(vertices_to_split[current_ps.depth], vertices_to_split[current_ps.depth], minimal_cell_reps_of_generators[index_in_fp_and_mcr])
            continue # main loop
        if backtrack:
            i = current_ps.depth
            current_ps.depth = min(max(first_kids_are_same - 1, label_and_current_indicator_same), current_kids_are_same - 1)
            if i == current_kids_are_same:
                continue # main loop
            if index_in_fp_and_mcr < len_of_fp_and_mcr - 1:
                index_in_fp_and_mcr += 1
            bitset_zero(fixed_points_of_generators[index_in_fp_and_mcr])
            bitset_zero(minimal_cell_reps_of_generators[index_in_fp_and_mcr])
            j = current_ps.depth
            current_ps.depth = i # just for mcr and fixed functions...
            for i from 0 <= i < n:
                if PS_is_mcr(current_ps, i):
                    bitset_set(minimal_cell_reps_of_generators[index_in_fp_and_mcr], i)
                    if PS_is_fixed(current_ps, i):
                        bitset_set(fixed_points_of_generators[index_in_fp_and_mcr], i)
            current_ps.depth = j
            if bitset_check(vertices_have_been_reduced[0], current_ps.depth):
                bitset_and(vertices_to_split[current_ps.depth], vertices_to_split[current_ps.depth], minimal_cell_reps_of_generators[index_in_fp_and_mcr])

    # End of main loop.

    if canonical_label:
        if input_group is NULL:
            for i from 0 <= i < n:
                output.relabeling[label_ps.entries[i]] = i
        else:
            for i from 0 <= i < n:
                output.relabeling[label_perm[i]] = i

    if work_space_prealloc is NULL:
        deallocate_agcl_work_space(work_space)

    return output














