How to use the spglib.standardize_cell function in spglib

structure: :class:`qmpy.Structure` object with a crystal structure.
        to_primitive: Boolean specifying whether to convert the input structure
            to a primitive unit cell.
        no_idealize: Boolean specifying whether to "idealize" lattice vectors,
            angles according to the ITC.
        symprec: Float with the Cartesian distance tolerance.
        verbosity: Integer with the level of standard output verbosity.

    Returns: :class:`qmpy.Structure` object with the standardized unit cell
        if successful, the input structure as is, otherwise.

    """
    _check_spglib_install()
    rev_lookup = dict(zip(structure.site_comp_indices,
                          structure.site_compositions))
    cell = spglib.standardize_cell(
        _structure_to_cell(structure),
        to_primitive=to_primitive,
        no_idealize=no_idealize,
        symprec=symprec
    )
    if not _check_spglib_success(cell,
                                 verbosity=verbosity):
        return structure
    _cell_to_structure(cell, structure, rev_lookup)
    return structure

idealize : bool
        Convert the cell into the spglib standardized form.
    tol : float
        Tolerance for floating point rounding errors.

    Returns
    -------
    primitive cell : object
        The primitive unit cell returned by spglib if one is found.
    """
    lattice = atoms.cell
    positions = atoms.get_scaled_positions()
    numbers = atoms.get_atomic_numbers()

    cell = (lattice, positions, numbers)
    cell = spglib.standardize_cell(
        cell, to_primitive=primitive, no_idealize=~idealize, symprec=tol)

    if cell is None:
        return atoms

    _lattice, _positions, _numbers = cell
    atoms = Gratoms(symbols=_numbers, cell=_lattice, pbc=atoms.pbc)
    atoms.set_scaled_positions(_positions)

    return atoms

print('')

print("[standardize_cell]")
print(" Standardize distorted rutile structure:")
print(" (to_primitive=0 and no_idealize=0)")
lattice, positions, numbers = spglib.standardize_cell(rutile_dist,
                                                      to_primitive=0,
                                                      no_idealize=0,
                                                      symprec=1e-1)
show_cell(lattice, positions, numbers)
print('')

print("[standardize_cell]")
print(" Standardize distorted rutile structure:")
print(" (to_primitive=0 and no_idealize=1)")
lattice, positions, numbers = spglib.standardize_cell(rutile_dist,
                                                      to_primitive=0,
                                                      no_idealize=1,
                                                      symprec=1e-1)
show_cell(lattice, positions, numbers)
print('')

print("[standardize_cell]")
print(" Standardize distorted silicon structure:")
print(" (to_primitive=1 and no_idealize=0)")
lattice, positions, numbers = spglib.standardize_cell(silicon_dist,
                                                      to_primitive=1,
                                                      no_idealize=0,
                                                      symprec=1e-1)
show_cell(lattice, positions, numbers)
print('')

structure_list = [s for s in structure_list if s.calc.results['energy'] < max_e]
        e_list.sort(key=lambda x: x[1], reverse=False)
        structure_list.sort(key=lambda x: x.calc.results['energy'], reverse=False)
        if total_struc != None and total_struc > 0:
            e_list = e_list[:total_struc]
            structure_list = structure_list[:total_struc]
        total_struc = len(e_list)
    elif i_mode == 4:
        total_struc = len(structure_list)

    if pbc == [True, True, True] or pbc == [True, True, False]:
        print('Analyzing symmetry')
    space_g_l = []
    for structure in structure_list:
        if pbc == [True, True, True]:
            structure.conventional_cell = standardize_cell(
                (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers), symprec=symprec)
            if structure.conventional_cell == None:
                structure.conventional_cell = structure
                structure.space_group = 'NULL(0)'
                space_g_l.append(1)
            else:
                structure.conventional_cell = Atoms(cell=structure.conventional_cell[0],
                                                    scaled_positions=structure.conventional_cell[1],
                                                    numbers=structure.conventional_cell[2], pbc=pbc)
                structure.space_group = get_spacegroup(
                    (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers),
                    symprec=symprec).replace(' ', '')
                space_g_l.append(int(get_spg_n(structure.space_group)))
        elif pbc == [False, False, False]:
            structure.conventional_cell = structure
            structure.space_group = 'P1(1)'

idealize : bool
        Convert the cell into the spglib standardized form.
    tol : float
        Tolerance for floating point rounding errors.

    Returns
    -------
    primitive cell : object
        The primitive unit cell returned by spglib if one is found.
    """
    lattice = atoms.cell
    positions = atoms.get_scaled_positions()
    numbers = atoms.get_atomic_numbers()

    cell = (lattice, positions, numbers)
    cell = spglib.standardize_cell(
        cell, to_primitive=primitive, no_idealize=~idealize, symprec=tol)

    if cell is None:
        return atoms

    _lattice, _positions, _numbers = cell
    atoms = Gratoms(symbols=_numbers, cell=_lattice, pbc=atoms.pbc)
    atoms.set_scaled_positions(_positions)

    return atoms

print('Analyzing symmetry')
        if r_cut_off == None:
            if pbc == [True, True, True]:
                r_cut_off = 9.0
            else:
                r_cut_off = 6.0
            # ccf_range = r_cut_off + extend_r
            # r_vector = np.linspace(0.0, ccf_range, int(ccf_range / ccf_step) + 2)
    elif r_cut_off == None:
        r_cut_off = 9.0
    ccf_range = r_cut_off + extend_r
    r_vector = np.linspace(0.0, ccf_range, int(ccf_range / ccf_step) + 2)
    space_g_l = []
    for structure in structure_list:
        if pbc == [True, True, True] or pbc == [True, True, False]:
            structure.conventional_cell = standardize_cell(
                (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers), symprec=symprec)
            if structure.conventional_cell == None:
                structure.conventional_cell = structure
                structure.space_group = 'NULL(0)'
                space_g_l.append(1)
            else:
                structure.conventional_cell = Atoms(cell=structure.conventional_cell[0],
                                                    scaled_positions=structure.conventional_cell[1],
                                                    numbers=structure.conventional_cell[2], pbc=pbc)
                structure.space_group = get_spacegroup(
                    (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers),
                    symprec=symprec).replace(' ', '')
                space_g_l.append(int(get_spg_n(structure.space_group)))
        elif pbc == [False, False, False]:
            structure.conventional_cell = structure
            structure.space_group = 'P1(1)'

))
            # structure_list[-1].e = e_list[ii][1]
            # structure_list[-1].n_structure = e_list[ii][2]
        # structure_list.sort(key=lambda x:x.e,reverse=False)
    elif i_mode == 2:
        print('Reading structure')
        total_struc = 0
        for root, dirs, files in os.walk('struc', topdown=True):
            for name in files:
                structure_list.append(read(os.path.join(root, name)))
                total_struc += 1

    print('Analyzing symmetry')
    space_g_l = []
    for structure in structure_list:
        structure.conventional_cell = standardize_cell(
            (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers), symprec=symprec)
        if structure.conventional_cell == None:
            structure.conventional_cell = structure
            structure.space_group = 'NULL(0)'
            space_g_l.append(0)
        else:
            structure.conventional_cell = Atoms(cell=structure.conventional_cell[0],
                                                scaled_positions=structure.conventional_cell[1],
                                                numbers=structure.conventional_cell[2], pbc=True)
            structure.space_group = get_spacegroup(
                (structure.cell, structure.get_scaled_positions(wrap=True), structure.numbers),
                symprec=symprec).replace(' ', '')
            space_g_l.append(int(get_spg_n(structure.space_group)))
        structure.conventional_cell.n_atom = len(structure.conventional_cell.numbers)
    if l_cif or l_poscar:
        if os.path.exists(dir_name):