.gitignore

@@ -1,4 +0,0 @@
-*~
-*.pyc
-__pycache__/
-.ipynb_checkpoints

README.md

@@ -1,5 +1,3 @@
-This project allows calculating knot invariants for linear combinations of iterated torus knots. 
-It was created as part of proof for the main lemma from a paper "On the slice genus of generalized algebraic knots" (Maria Marchwicka and Wojciech Politarczyk).
-
-To recreate calculations that were done for the proof see lemma.ipynb in notebooks.
-For a more detailed description see package documentation.
+This script calculates signature functions for knots (cable sums).
+The script can be run as a sage script from the terminal or used in interactive mode.
+A knot (cable sum) is encoded as a list where each element (also a list) corresponds to a cable knot.

cable_signature.sage

@@ -0,0 +1,637 @@
+#!/usr/bin/python
+import numpy as np
+import itertools as it
+from typing import Iterable
+from collections import Counter
+from sage.arith.functions import LCM_list
+import warnings
+import re
+import matplotlib.pyplot as plt
+import inspect
+
+# 9.11 (9.8)
+# 9.15 (9.9)
+PLOTS_DIR = "plots"
+
+class CableSummand():
+
+    def __init__(self, knot_as_k_values):
+        self.knot_as_k_values = knot_as_k_values
+
+        self._knot_description = self.get_summand_descrption(knot_as_k_values)
+        self._signature_as_function_of_theta = None
+
+
+    @staticmethod
+    def get_summand_descrption(knot_as_k_values):
+        description = ""
+        if knot_as_k_values[0] < 0:
+            description += "-"
+        description += "T("
+        for k in knot_as_k_values:
+            description += "2, " + str(2 * abs(k) + 1) + "; "
+        return description[:-2] + ")"
+
+    @property
+    def knot_description(self):
+        return self._knot_description
+
+    @property
+    def signature_as_function_of_theta(self):
+        if self._signature_as_function_of_theta is None:
+            self._signature_as_function_of_theta = \
+                    self.get_summand_signature_as_theta_function()
+        return self._signature_as_function_of_theta
+
+
+
+    @classmethod
+    def get_blanchfield_for_pattern(cls, k_n, theta=0):
+
+        msg = "Theorem on which this function is based, assumes " +\
+              "theta < k, where q = 2*k + 1 for pattern knot T(p, q)."
+        if theta == 0:
+            sf = cls.get_untwisted_signature_function(k_n)
+            return sf.square_root() + sf.minus_square_root()
+
+        k = abs(k_n)
+        assert theta <= k, msg
+        results = []
+
+        ksi = 1/(2 * k + 1)
+
+        counter = Counter()
+        # print("lambda_odd, i.e. (theta + e) % 2 != 0")
+        for e in range(1, k + 1):
+            if (theta + e) % 2 != 0:
+                counter[e * ksi] = 1 * sgn(k_n)
+                counter[1 - e * ksi] = -1 * sgn(k_n)
+
+                results.append((e * ksi, 1 * sgn(k_n)))
+                results.append((1 - e * ksi, -1 * sgn(k_n)))
+
+        # for example for k = 9 (q = 19) from this part we get
+        # for even theta
+        # 2/19: 1
+        # 4/19: 1
+        # 6/19: 1
+        # 8/19: 1
+        # 11/19: -1
+        # 13/19: -1
+        # 15/19: -1
+        # 17/19: -1
+        #
+        # for odd theta
+        # 1/19: 1
+        # 3/19: 1
+        # 5/19: 1
+        # 7/19: 1
+        # 9/19: 1
+        # 10/19: -1
+        # 12/19: -1
+        # 14/19: -1
+        # 16/19: -1
+        # 18/19: -1
+
+        # print("lambda_even")
+        # print("normal")
+        for e in range(1, theta):
+            if (theta + e) % 2 == 0:
+                results.append((e * ksi, 1 * sgn(k_n)))
+                results.append((1 - e * ksi, -1 * sgn(k_n)))
+        # print("reversed")
+        for e in range(theta + 1, k + 1):
+            if (theta + e) % 2 == 0:
+                results.append((e * ksi, -1 * sgn(k_n)))
+                results.append((1 - e * ksi, 1 * sgn(k_n)))
+
+        return SignatureFunction(values=results)
+
+    @classmethod
+    def get_satellite_part(cls, *knot_as_k_values, theta=0):
+        patt_k = knot_as_k_values[-1]
+        ksi = 1/(2 * abs(patt_k) + 1)
+
+        satellite_part = SignatureFunction()
+        # For each knot summand consider k values in reversed order,
+        # ommit k value for pattern.
+        for layer_num, k in enumerate(knot_as_k_values[:-1][::-1]):
+            sf = cls.get_untwisted_signature_function(k)
+            shift = theta * ksi * 2^layer_num
+            right_shift = sf >> shift
+            left__shift = sf << shift
+            for _ in range(layer_num):
+                right_shift = right_shift.double_cover()
+                left__shift = left__shift.double_cover()
+            satellite_part += right_shift + left__shift
+        return satellite_part
+
+    @staticmethod
+    def get_untwisted_signature_function(j):
+        # return the signature function of the T_{2, 2k+1} torus knot
+        k = abs(j)
+        q = 2 * k + 1
+        counter = Counter({(2 * a + 1)/(2 * q) : -sgn(j)
+                           for a in range(k)})
+        counter.update(Counter({(2 * a + 1)/(2 * q) : sgn(j)
+                           for a in range(k + 1, q)}))
+        return SignatureFunction(counter=counter)
+
+
+    def get_summand_signature_as_theta_function(self):
+        knot_as_k_values = self.knot_as_k_values
+        def get_summand_signture_function(theta):
+
+            patt_k = knot_as_k_values[-1]
+
+            # theta should not be larger than k for the pattern.
+            theta %= (2 * abs(patt_k) + 1)
+            theta = min(theta, 2 * abs(patt_k) + 1 - theta)
+
+            pattern_part = self.get_blanchfield_for_pattern(patt_k, theta)
+            satellite_part = self.get_satellite_part(*knot_as_k_values,
+                                                     theta=theta)
+            return pattern_part, satellite_part
+        get_summand_signture_function.__doc__ = \
+            get_summand_signture_function_docsting
+
+        return get_summand_signture_function
+
+    def get_file_name_for_summand_plot(self, theta=0):
+        if self.knot_as_k_values[0] < 0:
+            name = "inv_T_"
+        else:
+            name = "T_"
+        for k in self.knot_as_k_values:
+            name += str(abs(k)) + "_"
+        name += "_theta_" + str(theta)
+        return name
+
+
+    def plot_summand_for_theta(self, theta, save_path=None):
+        pp, sp = self.signature_as_function_of_theta(theta)
+        title = self.knot_description + ", theta = " + str(theta)
+        if save_path is not None:
+            file_name = self.get_file_name_for_summand_plot(theta)
+            save_path = os.path.join(save_path, file_name)
+        pp.plot_sum_with_other(sp, title=title, save_path=save_path)
+
+
+    def plot_summand(self):
+        range_limit = min(self.knot_as_k_values[-1] + 1, 3)
+        for theta in range(range_limit):
+            self.plot_summand_for_theta(theta)
+
+class CableSum():
+    def __init__(self, knot_sum):
+        self.knot_sum_as_k_valus = knot_sum
+        self.knot_summands = [CableSummand(k) for k in knot_sum]
+        self.signature_as_function_of_theta = \
+                        self.get_signature_as_function_of_theta()
+
+    def __call__(self, *thetas):
+        return self.signature_as_function_of_theta(*thetas)
+
+    def get_dir_name_for_plots(self, dir=None):
+        dir_name = ''
+        for knot in self.knot_summands:
+            if knot.knot_as_k_values[0] < 0:
+                dir_name += "inv_"
+            dir_name += "T_"
+            for k in knot.knot_as_k_values:
+                k = 2 * abs (k) + 1
+                dir_name += str(k) + "_"
+        dir_name = dir_name[:-1]
+        print(dir_name)
+        dir_path = os.getcwd()
+        if dir is not None:
+            dir_path = os.path.join(dir_path, dir)
+        dir_path = os.path.join(dir_path, dir_name)
+
+        if not os.path.isdir(dir_path):
+            os.mkdir(dir_path)
+        return dir_name
+
+    def plot_sum_for_theta_vector(self, thetas, save_to_dir=False):
+        if save_to_dir:
+            if not os.path.isdir(PLOTS_DIR):
+                os.mkdir(PLOTS_DIR)
+            dir_name = self.get_dir_name_for_plots(dir=PLOTS_DIR)
+            save_path = os.path.join(os.getcwd(), PLOTS_DIR)
+            save_path = os.path.join(save_path, dir_name)
+        else:
+            save_path = None
+        for i, knot in enumerate(self.knot_summands):
+            knot.plot_summand_for_theta(thetas[i], save_path=save_path)
+
+        pp, sp = self.signature_as_function_of_theta(*thetas)
+        title = self.knot_description + ", thetas = " + str(thetas)
+        if save_path is not None:
+            file_name = re.sub(r', ', '_', str(thetas))
+            file_name = re.sub(r'[\[\]]', '', str(file_name))
+            file_path = os.path.join(save_path, file_name)
+        pp.plot_sum_with_other(sp, title=title, save_path=file_path)
+
+
+        if save_path is not None:
+            file_path = os.path.join(save_path, "all_" + file_name)
+        sf_list = [knot.signature_as_function_of_theta(thetas[i])
+                    for i, knot in enumerate(self.knot_summands)]
+            #     pp, sp = knot.signature_as_function_of_theta(thetas[i])
+            #     (pp + sp) = sp.plot
+            #
+            # pp.plot_sum_with_other(sp, title=title, save_path=file_path)
+
+
+
+
+
+        return dir_name
+
+    def plot_all_summands(self):
+        for knot in self.knot_summands:
+            knot.plot_summand()
+
+
+    @property
+    def knot_description(self):
+        return self._knot_description
+
+    @property
+    def patt_k_list(self):
+        return self._patt_k_list
+
+    @property
+    def patt_q_list(self):
+        return self._patt_q_list
+
+    # q_order is LCM of all q values for pattern knots
+    @property
+    def q_order(self):
+        return self._q_order
+    @q_order.setter
+    def q_order(self, val):
+        self._q_order = val
+
+    @property
+    def knot_sum_as_k_valus(self):
+        return self._knot_sum_as_k_valus
+    @knot_sum_as_k_valus.setter
+    def knot_sum_as_k_valus(self, knot_sum):
+        self._knot_sum_as_k_valus = knot_sum
+        self._knot_description = self.get_knot_descrption(knot_sum)
+        self._patt_k_list = [abs(i[-1]) for i in knot_sum]
+        self._patt_q_list = [2 * i + 1 for i in self._patt_k_list]
+        if any(n not in Primes() for n in self._patt_q_list):
+            msg = "Incorrect q-vector. This implementation assumes that" + \
+                  " all last q values are prime numbers.\n" + \
+                  str(self._patt_q_list)
+            raise ValueError(msg)
+        self.q_order = LCM_list(self._patt_q_list)
+
+
+    def parse_thetas(self, *thetas):
+        summands_num = len(self.knot_sum_as_k_valus)
+        if not thetas:
+            thetas = summands_num * (0,)
+        elif len(thetas) == 1 and summands_num > 1:
+            if isinstance(thetas[0], Iterable):
+                if len(thetas[0]) >= summands_num:
+                    thetas = thetas[0]
+                elif not thetas[0]:
+                    thetas = summands_num * (0,)
+            elif thetas[0] == 0:
+                thetas = summands_num * (0,)
+            else:
+                msg = "This function takes at least " + str(summands_num) + \
+                      " arguments or no argument at all (" + str(len(thetas)) \
+                      + " given)."
+                raise TypeError(msg)
+        return tuple(thetas)
+
+
+    @staticmethod
+    def get_knot_descrption(knot_sum):
+        description = ""
+        for knot in knot_sum:
+            if knot[0] < 0:
+                description += "-"
+            description += "T("
+            for k in knot:
+                description += "2, " + str(2 * abs(k) + 1) + "; "
+            description = description[:-2] + ") # "
+        return description[:-3]
+
+    def get_signature_as_function_of_theta(self, **key_args):
+        if 'verbose' in key_args:
+            verbose_default = key_args['verbose']
+        else:
+            verbose_default = False
+        knot_desc = self.knot_description
+
+        def signature_as_function_of_theta(*thetas, **kwargs):
+            # print("\n\nsignature_as_function_of_theta " + knot_desc)
+            verbose = verbose_default
+            if 'verbose' in kwargs:
+                verbose = kwargs['verbose']
+            thetas = self.parse_thetas(*thetas)
+
+            satellite_part = SignatureFunction()
+            pattern_part = SignatureFunction()
+
+            # for each cable knot (summand) in cable sum apply theta
+            for i, knot in enumerate(self.knot_summands):
+                sfth = knot.signature_as_function_of_theta
+                pp, sp = sfth(thetas[i])
+                pattern_part += pp
+                satellite_part += sp
+            sf = pattern_part + satellite_part
+
+            if verbose:
+                print()
+                print(str(thetas))
+                print(sf)
+            assert sf.total_sign_jump() == 0
+            return pattern_part, satellite_part
+
+        signature_as_function_of_theta.__doc__ =\
+                            signature_as_function_of_theta_docstring
+        return signature_as_function_of_theta
+
+    def is_metabolizer(self, theta):
+        # Check if square alternating difference
+        # divided by last q value is integer.
+        result = sum(el^2 / self.patt_q_list[idx] * (-1)^idx
+                      for idx, el in enumerate(theta))
+        # for idx, el in enumerate(theta):
+        #     old_sum += (el^2 / self.patt_q_list[idx] * (-1)^idx)
+        return result.is_integer()
+
+    def is_signature_big_in_ranges(self, ranges_list):
+
+        for thetas in it.product(*ranges_list):
+
+            # Check only non-zero metabolizers.
+            if not self.is_metabolizer(thetas) or not any(thetas):
+                continue
+
+            signature_is_small = True
+            # Check if any element generated by thetas vector
+            # has a large signature.
+            for shift in range(1, self.q_order):
+                shifted_thetas = [shift * th for th in thetas]
+                pp, sp = self.signature_as_function_of_theta(*shifted_thetas)
+                sf = pp + sp
+                limit = 5 + np.count_nonzero(shifted_thetas)
+                extremum = abs(sf.extremum(limit=limit))
+                if shift > 1:
+                    print(shifted_thetas, end=" ")
+                    print(extremum)
+                if extremum > limit:
+                    signature_is_small = False
+                    break
+                elif shift == 1:
+                    print("*" * 10)
+                    print(shifted_thetas, end=" ")
+                    print(extremum)
+            if signature_is_small:
+                print("\n" * 10 + "!" * 1000)
+                return False
+        return True
+
+    def is_signature_big_for_all_metabolizers(self):
+        num_of_summands = len(self.knot_sum_as_k_valus)
+        if num_of_summands % 4:
+            f_name = self.is_signature_big_for_all_metabolizers.__name__
+            msg = "Function {}".format(f_name) + " is implemented only for " +\
+                  "knots that are direct sums of 4n direct summands."
+            raise ValueError(msg)
+
+        for shift in range(0, num_of_summands, 4):
+            ranges_list = num_of_summands * [range(0, 1)]
+            ranges_list[shift : shift + 3] = \
+                [range(0, i + 1) for i in self.patt_k_list[shift: shift + 3]]
+            ranges_list[shift + 3] = range(0, 2)
+            if not self.is_signature_big_in_ranges(ranges_list):
+                return False
+            else:
+                print("\nOK")
+        return True
+
+class CableTemplate():
+
+    def __init__(self, knot_formula, q_vector=None, k_vector=None,
+                 generate_q_vector=True, slice_candidate=True):
+        self._knot_formula = knot_formula
+        # q_i = 2 * k_i + 1
+        if k_vector is not None:
+            self.k_vector = k_vector
+        elif q_vector is not None:
+            self.q_vector = q_vector
+        elif generate_q_vector:
+            self.q_vector = self.get_q_vector(knot_formula, slice_candidate)
+
+    @property
+    def cable(self):
+        if self._cable is None:
+            msg = "q_vector for cable instance has not been set explicit. " + \
+                  "The variable is assigned a default value."
+            warnings.warn(msg)
+            self.fill_q_vector()
+        return self._cable
+
+    def fill_q_vector(self, q_vector=None, slice=True):
+        if q_vector is None:
+            q_vector =  self.get_q_vector(self.knot_formula)
+        self.q_vector = q_vector
+
+    @property
+    def knot_formula(self):
+        return self._knot_formula
+
+    @property
+    def k_vector(self):
+        return self._k_vector
+    @k_vector.setter
+    def k_vector(self, k):
+        self._k_vector = k
+        if self.extract_max(self.knot_formula) > len(k) - 1:
+            msg = "The vector for knot_formula evaluation is to short!"
+            msg += "\nk_vector " + str(k) + " \nknot_formula " \
+                + str(self.knot_formula)
+            raise IndexError(msg)
+
+        self.knot_sum_as_k_valus = eval(self.knot_formula)
+        self._cable = CableSum(self.knot_sum_as_k_valus)
+
+        self._q_vector = [2 * k_val + 1 for k_val in k]
+
+    @property
+    def q_vector(self):
+        return self._q_vector
+    @q_vector.setter
+    def q_vector(self, new_q_vector):
+        self.k_vector = [(q - 1)/2 for q in new_q_vector]
+
+    @staticmethod
+    def extract_max(string):
+        numbers = re.findall(r'\d+', string)
+        numbers = map(int, numbers)
+        return max(numbers)
+
+    @classmethod
+    def get_q_vector(cls, knot_formula, slice=True):
+        lowest_number = 2
+        q_vector = [0] * (cls.extract_max(knot_formula) + 1)
+        P = Primes()
+        for layer in cls.get_layers_from_formula(knot_formula)[::-1]:
+            for el in layer:
+                q_vector[el] = P.next(lowest_number)
+                lowest_number = q_vector[el]
+            lowest_number *= 4
+        return q_vector
+
+    @staticmethod
+    def get_layers_from_formula(knot_formula):
+        k_indices = re.sub(r'[k-]', '', knot_formula)
+        k_indices = re.sub(r'\[\d+\]', lambda x: x.group()[1:-1], k_indices)
+        k_indices = eval(k_indices)
+        number_of_layers = max(len(lst) for lst in k_indices)
+        layers = []
+        for i in range(1, number_of_layers + 1):
+            layer = set()
+            for lst in k_indices:
+                if len(lst) >= i:
+                    layer.add(lst[-i])
+            layers.append(layer)
+        return layers
+
+    def add_with_shift(self, other):
+        shift = self.extract_max(self.knot_formula) + 1
+        o_formula = re.sub(r'\d+', lambda x: str(int(x.group()) + shift),
+                           other.knot_formula)
+        return self + CableTemplate(o_formula)
+
+
+    def __add__(self, other):
+        s_formula = self.knot_formula
+        o_formula = other.knot_formula
+        knot_formula = s_formula[:-1] + ",\n" + o_formula[1:]
+        cable_template = CableTemplate(knot_formula)
+        return cable_template
+
+
+
+def mod_one(n):
+    return n - floor(n)
+
+
+# CableSum.get_knot_descrption.__doc__ = \
+#     """
+#     Arguments:
+#         arbitrary number of lists of numbers, each list encodes a single cable.
+#     Examples:
+#         sage: get_knot_descrption([1, 3], [2], [-1, -2], [-3])
+#         'T(2, 3; 2, 7) # T(2, 5) # -T(2, 3; 2, 5) # -T(2, 7)'
+#     """
+
+CableSum.get_signature_as_function_of_theta.__doc__ = \
+    """
+    Function intended to construct signature function for a connected
+    sum of multiple cables with varying theta parameter values.
+    Accept arbitrary number of arguments (depending on number of cables in
+    connected sum).
+    Each argument should be given as list of integer representing
+    k - parameters for a cable: parameters k_i (i=1,.., n-1) for satelit knots
+    T(2, 2k_i + 1) and - the last one - k_n for a pattern knot T(2, 2k_n + 1).
+    Returns a function that will take theta vector as an argument and return
+    an object SignatureFunction.
+
+    To calculate signature function for a cable sum and a theta values vector,
+    use as below.
+
+    sage: signature_function_generator = get_signature_as_function_of_theta(
+                                             [1, 3], [2], [-1, -2], [-3])
+    sage: sf = signature_function_generator(2, 1, 2, 2)
+    sage: print(sf)
+    0: 0
+    5/42: 1
+    1/7: 0
+    1/5: -1
+    7/30: -1
+    2/5: 1
+    3/7: 0
+    13/30: -1
+    19/42: -1
+    23/42: 1
+    17/30: 1
+    4/7: 0
+    3/5: -1
+    23/30: 1
+    4/5: 1
+    6/7: 0
+    37/42: -1
+
+    Or like below.
+    sage: print(get_signature_as_function_of_theta([1, 3], [2], [-1, -2], [-3]
+                                                )(2, 1, 2, 2))
+    0: 0
+    1/7: 0
+    1/6: 0
+    1/5: -1
+    2/5: 1
+    3/7: 0
+    1/2: 0
+    4/7: 0
+    3/5: -1
+    4/5: 1
+    5/6: 0
+    6/7: 0
+    """
+
+get_summand_signture_function_docsting = \
+    """
+    This function returns SignatureFunction for previously defined single
+    cable T_(2, q) and a theta given as an argument.
+    The cable was defined by calling function
+    get_summand_signature_as_theta_function(*arg)
+    with the cable description as an argument.
+    It is an implementaion of the formula:
+        Bl_theta(K'_(2, d)) =
+            Bl_theta(T_2, d) + Bl(K')(ksi_l^(-theta) * t)
+            + Bl(K')(ksi_l^theta * t)
+    """
+
+signature_as_function_of_theta_docstring = \
+    """
+    Arguments:
+
+    Returns object of SignatureFunction class for a previously defined
+    connected sum of len(arg) cables.
+    Accept len(arg) arguments: for each cable one theta parameter.
+    If call with no arguments, all theta parameters are set to be 0.
+    """
+#
+# CableSummand.get_blanchfield_for_pattern.__doc__ = \
+#     """
+#     Arguments:
+#         k_n:    a number s.t. q_n = 2 * k_n + 1, where
+#                 T(2, q_n) is a pattern knot for a single cable from a cable sum
+#         theta:  twist/character for the cable (value form v vector)
+#     Return:
+#         SignatureFunction created for pattern signature function
+#         for a given cable and theta/character
+#     Based on:
+#         Proposition 9.8. in Twisted Blanchfield Pairing
+#         (https://arxiv.org/pdf/1809.08791.pdf)
+#     """
+
+# CableSummand.get_summand_signature_as_theta_function.__doc__ = \
+#     """
+#     Argument:
+#         n integers that encode a single cable, i.e.
+#         values of q_i for T(2,q_0; 2,q_1; ... 2, q_n)
+#     Return:
+#         a function that returns SignatureFunction for this single cable
+#         and a theta given as an argument
+#     """

gaknot/__init__.py

@@ -1,64 +0,0 @@
-#!/usr/bin/env python3
-
-r"""calculations of signature function and sigma invariant of generalized algebraic knots (GA-knots)
-
-
-The package was used to prove Lemma 3.2 from a paper
-'On the slice genus of generalized algebraic knots' Maria Marchwicka and Wojciech Politarczyk).
-It contains the following submodules.
-    1) main.sage - with function prove_lemma
-    2) signature.sage - contains SignatureFunction class;
-       it encodes twisted and untwisted signature functions
-       of knots and allows to perform algebraic operations on them.
-    3) cable_signature.sage - contains the following classes:
-        a) CableSummand - it represents a single cable knot,
-        b) CableSum - it represents a cable sum, i. e. linear combination of single cable knots;
-           since the signature function and sigma invariant are additive under connected sum,
-           the class use calculations from CableSummand objects,
-        c) CableTemplate - it represents a scheme for a cable sums.
-
-"""
-
-
-from .utility import import_sage
-import os
-
-package = __name__.split('.')[0]
-dirname = os.path.dirname
-path = dirname(dirname(__file__))
-import_sage('signature', package=package, path=path)
-import_sage('cable_signature', package=package, path=path)
-import_sage('main', package=package, path=path)
-
-from .main import prove_lemma
-
-
-# EXAMPLES::
-#
-# sage: eval_cable_for_null_signature([[1, 3], [2], [-1, -2], [-3]])
-#
-# T(2, 3; 2, 7) # T(2, 5) # -T(2, 3; 2, 5) # -T(2, 7)
-# Zero cases: 1
-# All cases: 1225
-# Zero theta combinations:
-# (0, 0, 0, 0)
-#
-# sage:
-#
-# The numbers given to the function eval_cable_for_null_signature are k-values
-# for each component/cable in a direct sum.
-#
-# To calculate signature function for a knot and a theta value, use function
-# get_signature_as_function_of_theta (see help/docstring for details).
-#
-# About notation:
-# Cables that we work with follow a schema:
-#     T(2, q_1; 2, q_2; 2, q_4) # -T(2, q_2; 2, q_4) #
-#             # T(2, q_3; 2, q_4) # -T(2, q_1; 2, q_3; 2, q_4)
-# In knot_formula each k[i] is related with some q_i value, where
-# q_i = 2*k[i] + 1.
-# So we can work in the following steps:
-# 1) choose a schema/formula by changing the value of knot_formula
-# 2) set each q_i all or choose range in which q_i should varry
-# 3) choose vector v / theta vector.
-#

gaknot/cable_signature.sage

@@ -1,863 +0,0 @@
-#!/usr/bin/env sage -python
-
-import numpy as np
-import itertools as it
-import warnings
-import logging
-import re
-import ast
-from typing import Iterable
-from collections import Counter
-from sage.arith.functions import LCM_list
-# import importlib
-
-
-
-# preparsing sage script and import as module
-if __name__ == '__main__':  # TBD - check is this is optimal
-    from utility import import_sage
-    package = None
-    path = ''
-else:  # called from package
-    from .utility import import_sage
-    package = os.path.join( __name__.split('.')[0])
-    path = '../'
-sg = import_sage('signature', package=package, path=path)
-
-# constants - which invariants should be calculate
-SIGMA = 0
-SIGNATURE = 1
-
-
-# #############################################################################
-# 9.11 (9.8)
-# 9.15 (9.9)
-PLOTS_DIR = "../plots"
-
-
-class CableSummand:
-
-    def __init__(self, knot_as_k_values, verbose=False):
-
-        self.verbose = verbose
-        self.knot_as_k_values = knot_as_k_values
-        self.knot_description = self.get_summand_descrption(knot_as_k_values)
-        self.signature_as_function_of_theta = \
-                                self.get_summand_signature_as_theta_function()
-        self.sigma_as_function_of_theta = self.get_sigma_as_function_of_theta()
-
-    @staticmethod
-    def get_summand_descrption(knot_as_k_values):
-        description = ""
-        if knot_as_k_values[0] < 0:
-            description += "-"
-        description += "T("
-        for k in knot_as_k_values:
-            description += "2, " + str(2 * abs(k) + 1) + "; "
-        return description[:-2] + ")"
-
-    @classmethod
-    def get_blanchfield_for_pattern(cls, k_n, theta=0):
-
-        msg = "Theorem on which this function is based, assumes " +\
-              "theta < k, where q = 2*k + 1 for pattern knot T(p, q)."
-        if theta == 0:
-            sf = cls.get_untwisted_signature_function(k_n)
-            return sf.square_root() + sf.minus_square_root()
-
-        k = abs(k_n)
-        assert theta <= k, msg
-
-        results = []
-        ksi = 1/(2 * k + 1)
-
-        # print("lambda_odd, i.e. (theta + e) % 2 != 0")
-        for e in range(1, k + 1):
-            if (theta + e) % 2 != 0:
-                results.append((e * ksi, 1 * sgn(k_n)))
-                results.append((1 - e * ksi, -1 * sgn(k_n)))
-
-        # for example for k = 9 (q = 19) from this part we get
-        # for even theta
-        # 2/19: 1
-        # 4/19: 1
-        # 6/19: 1
-        # 8/19: 1
-        # 11/19: -1
-        # 13/19: -1
-        # 15/19: -1
-        # 17/19: -1
-        #
-        # for odd theta
-        # 1/19: 1
-        # 3/19: 1
-        # 5/19: 1
-        # 7/19: 1
-        # 9/19: 1
-        # 10/19: -1
-        # 12/19: -1
-        # 14/19: -1
-        # 16/19: -1
-        # 18/19: -1
-
-        # print("lambda_even")
-        # print("normal")
-        for e in range(1, theta):
-            if (theta + e) % 2 == 0:
-                results.append((e * ksi, 1 * sgn(k_n)))
-                results.append((1 - e * ksi, -1 * sgn(k_n)))
-        # print("reversed")
-        for e in range(theta + 1, k + 1):
-            if (theta + e) % 2 == 0:
-                results.append((e * ksi, -1 * sgn(k_n)))
-                results.append((1 - e * ksi, 1 * sgn(k_n)))
-
-        return sg.SignatureFunction(values=results)
-
-    @classmethod
-    def get_satellite_part(cls, *knot_as_k_values, theta=0):
-        patt_k = knot_as_k_values[-1]
-        ksi = 1/(2 * abs(patt_k) + 1)
-
-        satellite_part = sg.SignatureFunction()
-        # For each knot summand consider k values in reversed order,
-        # ommit k value for pattern.
-        for layer_num, k in enumerate(knot_as_k_values[:-1][::-1]):
-            sf = cls.get_untwisted_signature_function(k)
-            shift = theta * ksi * 2^layer_num
-            right_shift = sf >> shift
-            left__shift = sf << shift
-            for _ in range(layer_num):
-                right_shift = right_shift.double_cover()
-                left__shift = left__shift.double_cover()
-            satellite_part += right_shift + left__shift
-        return satellite_part
-
-    @staticmethod
-    def get_untwisted_signature_function(k=None, q=None):
-        # return the signature function of the T_{2, 2k+1} torus knot
-
-        if q is not None:
-            signum = sign(q)
-            q = abs(q)
-            k = (q - 1)/2
-        elif k is not None:
-            signum = sign(k)
-            k = abs(k)
-            q = 2 * k + 1
-        else:
-            raise ValueError('k or q value must be given')
-
-        counter = Counter({(2 * a + 1)/(2 * q): -signum
-                           for a in range(k)})
-        counter.update(Counter({(2 * a + 1)/(2 * q): signum
-                           for a in range(k + 1, q)}))
-        return sg.SignatureFunction(counter=counter)
-
-    def get_summand_signature_as_theta_function(self):
-        # knot_as_k_values = self.knot_as_k_values
-        def get_summand_signture_function(theta):
-
-            patt_k = self.knot_as_k_values[-1]
-
-            # theta should not be larger than k for the pattern.
-            theta %= (2 * abs(patt_k) + 1)
-            theta = min(theta, 2 * abs(patt_k) + 1 - theta)
-
-            pattern_part = self.get_blanchfield_for_pattern(patt_k, theta)
-            satellite_part = self.get_satellite_part(*self.knot_as_k_values,
-                                                     theta=theta)
-            sf = satellite_part + pattern_part
-
-            satellite_part.plot_title = self.knot_description + \
-                                        ", theta = " + str(theta) + \
-                                         ", satellite part."
-            pattern_part.plot_title = self.knot_description + \
-                                      ", theta = " + str(theta) + \
-                                      ", pattern part."
-            sf.plot_title = self.knot_description +\
-                            ", theta = " + str(theta)
-
-            return pattern_part, satellite_part, sf
-        get_summand_signture_function.__doc__ = \
-            get_summand_signture_function_docsting
-
-        return get_summand_signture_function
-
-    def get_file_name_for_summand_plot(self, theta=0):
-        if self.knot_as_k_values[0] < 0:
-            name = "inv_T_"
-        else:
-            name = "T_"
-        for k in self.knot_as_k_values:
-            name += str(abs(k)) + "_"
-        name += "_theta_" + str(theta)
-        return name
-
-    def plot_summand_for_theta(self, theta, save_path=None):
-        pp, sp, sf = self.signature_as_function_of_theta(theta)
-        title = self.knot_description + ", theta = " + str(theta)
-        if save_path is not None:
-            file_name = self.get_file_name_for_summand_plot(theta)
-            save_path = os.path.join(save_path, file_name)
-        sg.SignaturePloter.plot_sum_of_two(pp, sp, title=title,
-                                            save_path=save_path)
-
-    def plot_summand_sigma(self):
-        sigma = self.sigma_as_function_of_theta
-        # pattern part
-        th_values = list(range(abs(self.knot_as_k_values[-1]) + 1))
-        y = [sigma(th)[0] for th in th_values]
-        print("plot_summand_sigma")
-        print(th_values)
-        print(y)
-
-        # satellite_part
-        patt_k = self.knot_as_k_values[-1]
-        patt_q = 2 * abs(patt_k) + 1
-        ksi = 1/patt_q
-        x = []
-        s = self.get_untwisted_signature_function
-        list_of_signatue_functions = [s(k) for k in self.knot_as_k_values[:-1]]
-        for i, k in enumerate(self.knot_as_k_values[:-1][::-1]):
-            layer_num = i + 1
-            x.append(ksi * layer_num)
-        print("\nx")
-        print(x)
-        print(th_values)
-        print("\nx product")
-        x = list(set(it.product(x, th_values)))
-        x = [(a * b) for (a, b) in x]
-        print(x)
-
-
-    def print_sigma_as_function_of_theta(self, theta):
-        if not theta:
-            return
-
-        # theta should not be larger than q for the pattern.
-        patt_k = self.knot_as_k_values[-1]
-
-        patt_q = 2 * abs(patt_k) + 1
-        theta %= patt_q
-
-        ksi = 1/patt_q
-
-        # satellite part (Levine-Tristram signatures)
-        print(3 * "\n" + 10 * "#" + " " + self.knot_description +
-              " " + 10 * "#" + "\n")
-
-        satellite_part = 0
-        for layer_num, k in enumerate(self.knot_as_k_values[::-1]):
-
-            sigma_q = self.get_untwisted_signature_function(k)
-            arg = ksi * theta * layer_num
-            sp = sigma_q(arg)
-            satellite_part += 2 * sp
-
-            if details and arg:
-                label = "ksi * theta * layer_num = " + str(arg)
-                title = self.knot_description + ", layer " + str(layer_num)
-                title += ", theta = " + str(theta)
-                sigma_q.plot(special_point=(mod_one(arg), sp),
-                             special_label=label,
-                             title=title,)
-
-        pp = (-patt_q + 2 * theta - 2 * (theta^2/patt_q)) * sign(patt_k)
-        sigma = pp + satellite_part
-        print(self.knot_description + ", theta = " + str(theta))
-        print("pp = " + str(pp), end=', ')
-        print("satellite_part = " + str(satellite_part) + "\n")
-
-    def get_sigma_as_function_of_theta(self):
-
-        patt_k = self.knot_as_k_values[-1]
-        patt_q = 2 * abs(patt_k) + 1
-        ksi = 1/patt_q
-
-        def sigma_as_function_of_theta(theta):
-            if theta == 0:
-                return 0, 0, 0
-
-            # theta should not be larger than q for the pattern.
-            patt_k = self.knot_as_k_values[-1]
-            theta %= (2 * abs(patt_k) + 1)
-
-            satellite_part = 0
-            for i, k in enumerate(self.knot_as_k_values[:-1][::-1]):
-                layer_num = i + 1
-                sigma_q = self.get_untwisted_signature_function(k)
-                sp = 2 * sigma_q(ksi * theta * layer_num)
-                satellite_part += sp
-            if theta:
-                pp = (-patt_q + 2 * theta - 2 * (theta^2/patt_q)) * sign(patt_k)
-            else:
-                pp = 0
-            return pp, satellite_part, pp + satellite_part
-        return sigma_as_function_of_theta
-
-
-class CableSum:
-
-    def __init__(self, knot_sum, verbose=False):
-
-        self.verbose = verbose
-        self.knot_sum_as_k_valus = knot_sum
-        self.knot_description = self.get_knot_descrption(knot_sum)
-        self.patt_k_list = [abs(i[-1]) for i in knot_sum]
-        self.patt_q_list = [2 * i + 1 for i in self.patt_k_list]
-
-        if any(n not in Primes() for n in self.patt_q_list):
-            msg = "Incorrect k- or q-vector. This implementation assumes that"\
-                  + " all last q values are prime numbers.\n" + \
-                  str(self.patt_q_list)
-            raise ValueError(msg)
-        self.q_order = LCM_list(self.patt_q_list)
-
-        self.knot_summands = [CableSummand(k, verbose) for k in knot_sum]
-        self.signature_as_function_of_theta = \
-                        self.get_signature_as_function_of_theta()
-        self.sigma_as_function_of_theta = \
-                        self.get_sigma_as_function_of_theta()
-
-
-    def __call__(self, *thetas):
-        return self.signature_as_function_of_theta(*thetas)
-
-    def get_dir_name_for_plots(self, dir=None):
-        dir_name = ''
-        for knot in self.knot_summands:
-            if knot.knot_as_k_values[0] < 0:
-                dir_name += "inv_"
-            dir_name += "T_"
-            for k in knot.knot_as_k_values:
-                k = 2 * abs (k) + 1
-                dir_name += str(k) + "_"
-        dir_name = dir_name[:-1]
-        print(dir_name)
-        dir_path = os.getcwd()
-        if dir is not None:
-            dir_path = os.path.join(dir_path, dir)
-        dir_path = os.path.join(dir_path, dir_name)
-
-        if not os.path.isdir(dir_path):
-            os.mkdir(dir_path)
-        return dir_name
-
-    def plot_sum_for_theta_vector(self, thetas, save_to_dir=False):
-        if save_to_dir:
-            if not os.path.isdir(PLOTS_DIR):
-                os.mkdir(PLOTS_DIR)
-            dir_name = self.get_dir_name_for_plots(dir=PLOTS_DIR)
-            save_path = os.path.join(os.getcwd(), PLOTS_DIR)
-            save_path = os.path.join(save_path, dir_name)
-        else:
-            save_path = None
-
-        # for theta, knot in zip(thetas, self.knot_summands):
-        #     knot.plot_summand_for_theta(thetas, save_path=save_path)
-
-        # pp, sp, sf = self.signature_as_function_of_theta(*thetas)
-        # title = self.knot_description + ", thetas = " + str(thetas)
-        # if save_path is not None:
-        #     file_name = re.sub(r', ', '_', str(thetas))
-        #     file_name = re.sub(r'[\[\]]', '', str(file_name))
-        #     file_path = os.path.join(save_path, file_name)
-        # sg.SignaturePloter.plot_sum_of_two(pp, sp, title=title,
-        #                                      save_path=file_path)
-        #
-        # if save_path is not None:
-        #     file_path = os.path.join(save_path, "all_" + file_name)
-        # sf_list = [knot.signature_as_function_of_theta(thetas[i])[2]
-        #             for i, knot in enumerate(self.knot_summands)]
-        # sg.SignaturePloter.plot_many(*sf_list, cols=2)
-            #     pp, sp, sf = knot.signature_as_function_of_theta(thetas[i])
-            #     (pp + sp) = sp.plot
-            #
-            # sg.SignatureFunction.plot_sum_of_two(pp, sp, title=title,
-            #                                      save_path=file_path)
-
-
-        return dir_name
-
-    def plot_sigma_for_summands(self):
-        for knot in self.knot_summands:
-            knot.plot_summand_sigma()
-
-    def parse_thetas(self, *thetas):
-        summands_num = len(self.knot_sum_as_k_valus)
-        if not thetas:
-            thetas = summands_num * (0,)
-        elif len(thetas) == 1 and summands_num > 1:
-            if isinstance(thetas[0], Iterable):
-                if len(thetas[0]) >= summands_num:
-                    thetas = thetas[0]
-                elif not thetas[0]:
-                    thetas = summands_num * (0,)
-            elif thetas[0] == 0:
-                thetas = summands_num * (0,)
-            else:
-                msg = "This function takes at least " + str(summands_num) + \
-                      " arguments or no argument at all (" + str(len(thetas)) \
-                      + " given)."
-                raise TypeError(msg)
-        return tuple(thetas)
-
-    @staticmethod
-    def get_knot_descrption(knot_sum):
-
-        """
-        Arguments:
-            arbitrary number of lists of numbers,
-            each list encodes a single cable.
-        Examples:
-            sage: get_knot_descrption([1, 3], [2], [-1, -2], [-3])
-            'T(2, 3; 2, 7) # T(2, 5) # -T(2, 3; 2, 5) # -T(2, 7)'
-        """
-
-        description = ""
-        for knot in knot_sum:
-            if knot[0] < 0:
-                description += "-"
-            description += "T("
-            for k in knot:
-                description += "2, " + str(2 * abs(k) + 1) + "; "
-            description = description[:-2] + ") # "
-        return description[:-3]
-
-    def get_sigma_as_function_of_theta(self, verbose=None):
-        default_verbose = verbose or self.verbose
-
-        def sigma_as_function_of_theta(*thetas, verbose=None, **kwargs):
-
-            verbose = verbose or default_verbose
-            thetas = self.parse_thetas(*thetas)
-            sigma = 0
-            for th, knot in zip(thetas, self.knot_summands):
-                _, _, s = knot.sigma_as_function_of_theta(th)
-                sigma += s
-            return sigma
-
-        return sigma_as_function_of_theta
-
-    def get_signature_as_function_of_theta(self, **key_args):
-        if 'verbose' in key_args:
-            verbose_default = key_args['verbose']
-        else:
-            verbose_default = False
-        knot_desc = self.knot_description
-
-        def signature_as_function_of_theta(*thetas, **kwargs):
-            # print("\n\nsignature_as_function_of_theta " + knot_desc)
-            verbose = verbose_default
-            if 'verbose' in kwargs:
-                verbose = kwargs['verbose']
-            thetas = self.parse_thetas(*thetas)
-
-            satellite_part = sg.SignatureFunction()
-            pattern_part = sg.SignatureFunction()
-
-            # for each cable knot (summand) in cable sum apply theta
-            for th, knot in zip(thetas, self.knot_summands):
-                pp, sp, _ = knot.signature_as_function_of_theta(th)
-                pattern_part += pp
-                satellite_part += sp
-
-
-            sf = pattern_part + satellite_part
-
-            if verbose:
-                print()
-                print(str(thetas))
-                print(sf)
-            assert sf.total_sign_jump() == 0
-            return pattern_part, satellite_part, sf
-
-        signature_as_function_of_theta.__doc__ =\
-                            signature_as_function_of_theta_docstring
-        return signature_as_function_of_theta
-
-    def get_sign_ext_for_theta(self, thetas, limit):
-        _, _, sf = self.signature_as_function_of_theta(*thetas)
-        return sf.extremum(limit=limit)[1]
-
-    def is_metabolizer(self, theta):
-        # Check if square alternating difference
-        # divided by last q value is integer.
-        result = sum(el^2 / self.patt_q_list[idx] * (-1)^idx
-                      for idx, el in enumerate(theta))
-        return result.is_integer()
-
-    def is_function_big_in_ranges(self, ranges_list, invariant=SIGMA,
-                                  verbose=None, details=False,
-                                  p_part_order=None):
-        verbose = verbose or self.verbose
-        p_part_order = p_part_order or self.q_order
-
-        if invariant == SIGNATURE:
-            get_invariant = self.get_sign_ext_for_theta
-            name = "signature (extremum)"
-        else:
-            get_invariant = self.sigma_as_function_of_theta
-            name = "sigma value"
-
-        if verbose:
-            msg = "\nCalculating {}-primary part.".format(p_part_order)
-            print(msg)
-
-        logging.info(str(ranges_list))
-
-
-        for thetas in it.product(*ranges_list):
-
-            # Check only non-zero metabolizers.
-            if not self.is_metabolizer(thetas) or not any(thetas):
-                continue
-
-            function_is_small = True
-            # Check if any element generated by thetas vector
-            # has a large signature or sigma.
-            for shift in range(1, p_part_order):
-                shifted_thetas = \
-                            [(shift * th) % p_part_order for th in thetas]
-                limit = 5 + np.count_nonzero(shifted_thetas)
-                inv_value = get_invariant(shifted_thetas, limit=limit)
-                abs_value = abs(inv_value)
-
-                if verbose:
-                    if shift == 1:
-                        print("\n" + "*" * 10)
-                        print("[ character ] " + name)
-                    print(shifted_thetas, end=" ")
-                    print(inv_value)
-
-                if abs_value > limit:
-                    function_is_small = False
-                    if details:
-                        self.print_calculations_for_sigma(*shifted_thetas)
-                    break
-            if function_is_small:
-                if verbose and invariant == SIGMA:
-                    msg = "For an element x = " + str(thetas)
-                    msg += " there does not exist any shift such that "
-                    msg += "|sigma(K, shift * x)| > {}.\n".format(limit)
-                    msg += "We can not give any lower bound for 4-genus."
-                    print(msg)
-                return False
-        return True
-
-    def print_calculations_for_sigma(self, *thetas):
-
-        print("Calculation details for a cable sum:\n" +
-              self.knot_description + "\nand theta vector: " +
-              str(thetas) + "\n")
-
-        for i, (th, knot) in enumerate(zip(thetas, self.knot_summands)):
-            print("{}. {}, theta = {}".format(i + 1, knot.knot_description, th))
-            if not th:
-                continue
-            patt_k = knot.knot_as_k_values[-1]
-            q = 2 * abs(patt_k) + 1
-            th %= q
-            if patt_k > 0:
-                print("Pattern part = pp")
-            else:
-                print("Pattern part = -pp")
-
-            print("pp = -q  + 2 * theta * (q - theta)/q =")
-            print("   = -{} + 2 * {}     *  ({}  - {} )/{} =".format(
-                         q,      th, q,  th, q))
-            print("   = -{} +      {}     *  ({}       )/{} =".format(
-                         q,   2 * th, q - th, q))
-            print("   = -{} + {} * {} = ".format(
-                         q,   2 * th, (q - th)/ q))
-            print("   = -{} +  {}  = ".format(
-                         q,   2 * th * (q - th)/ q))
-            print("   = {}  ".format(
-                        -q + (2 * th * (q - th)/ q)))
-
-            pp = (-q + 2 * th - 2 * (th^2/q)) * sign(patt_k)
-            sigma = knot.sigma_as_function_of_theta(th)
-            print("Pattern part = {} ~ {}".format(sigma[0],int(sigma[0])))
-            print("Satellite part = {}".format(sigma[1]))
-            print("Sigma = {} ~ {}\n".format(sigma[2], int(sigma[2])))
-
-    # function that proves the main lemma
-    def is_function_big_for_all_metabolizers(self, invariant=SIGMA,
-                                             verbose=False, details=False):
-        logging.info("start of is_function_big_for_all_metabolizers")
-        if invariant == SIGNATURE:
-            name = "signature (extremum)"
-        else:
-            name = "sigma value"
-
-        num_of_summands = len(self.knot_sum_as_k_valus)
-        if num_of_summands % 4:
-            f_name = self.is_signature_big_for_all_metabolizers.__name__
-            msg = "Function {}".format(f_name) + " is implemented only for " +\
-                  "knots that are direct sums of 4n direct summands."
-            raise ValueError(msg)
-
-        # check each p-primary part separately
-        logging.info("number of summands is {}".format(num_of_summands))
-        for shift in range(0, num_of_summands, 4):
-
-            logging.info("shift is {}".format(shift))
-            p_part_order = 2 * self.patt_k_list[shift] + 1
-
-            logging.info("set character (twist) to be zero for all summands")
-            ranges_list = num_of_summands * [range(1)]
-            logging.info(str(ranges_list))
-
-
-            # change ranges for all but one character for current p-primary part
-            ranges_list[shift + 1 : shift + 4] = 3 * [range(p_part_order)]
-
-            # change range for first character in current p-primary part
-            # this one is consider to be 0 or 1
-            # For any characters combinations (vectors) [a_1, a_2, a_3, a_4]
-            # where a_4 != 0 exists such a k < p that k * a_1 % p == 1.
-            ranges_list[shift] = range(0, 2)
-            logging.info("\n\ncall is_function_big_in_ranges with values")
-            logging.info(str(ranges_list))
-
-            if not self.is_function_big_in_ranges(ranges_list, invariant,
-                                                  p_part_order=p_part_order,
-                                                  verbose=verbose,
-                                                  details=details):
-                logging.info("Not proven.")
-                return False
-        if verbose and invariant == SIGMA:
-            msg = "For each p-primery part for each vector x there exist "
-            msg += "a number 0 < shift < p such that "
-            msg += "sigma(K, shift * x) > 5 + eta(K, shift * x)."
-            print(msg)
-            print("q.e.d.")
-        return True
-
-
-class CableTemplate:
-
-    def __init__(self, knot_formula, q_vector=None, k_vector=None,
-                 generate_q_vector=True, algebraic=True, verbose=False):
-        self.verbose = verbose
-        self._knot_formula = knot_formula
-        # q_i = 2 * k_i + 1
-        if k_vector is not None:
-            self.k_vector = k_vector
-        elif q_vector is not None:
-            self.q_vector = q_vector
-        elif generate_q_vector:
-            self.q_vector = self.get_q_vector(algebraic=slice)
-        self.templete_description = self.get_template_descrption()
-
-
-    def __str__(self):
-        return self.templete_description
-
-    def get_template_descrption(self):
-        k_indices = re.sub(r'[k ]', '', self.knot_formula)
-        k_indices = re.sub(r'\[\d+\]', lambda x: x.group()[1:-1], k_indices)
-        k_indices = ast.literal_eval(k_indices)
-        description = ""
-        for summand in k_indices :
-                part = ""
-                if summand[0] < 0:
-                    part += "-"
-                part += "T("
-                for k in summand:
-                    part += "2, q_" + str(abs(k)) + "; "
-                description += part[:-2] + ") # "
-        return description[:-3]
-
-    @property
-    def cable(self):
-        if self._cable is None:
-            msg = "q_vector for cable instance has not been set explicit. " + \
-                  "The variable is assigned a default value."
-            warnings.warn(msg)
-            self.fill_q_vector()
-        return self._cable
-
-    def fill_q_vector(self, q_vector=None, algebraic=True, lowest_number=2):
-        self.q_vector = q_vector or self.get_q_vector(slice, lowest_number)
-
-    @property
-    def knot_formula(self):
-        return self._knot_formula
-
-    @property
-    def k_vector(self):
-        return self._k_vector
-    @k_vector.setter
-    def k_vector(self, k):
-        self._k_vector = k
-        if self.extract_max(self.knot_formula) > len(k) - 1:
-            msg = "The vector for knot_formula evaluation is to short!"
-            msg += "Note that we count from 0 (not 1)."
-            msg += "\nk_vector " + str(k) + " \nknot_formula " \
-                + str(self.knot_formula)
-            raise IndexError(msg)
-
-        self.knot_sum_as_k_valus = eval(self.knot_formula)
-        self._cable = CableSum(self.knot_sum_as_k_valus, verbose=self.verbose)
-        self._q_vector = [2 * k_val + 1 for k_val in k]
-
-    @property
-    def q_vector(self):
-        return self._q_vector
-    @q_vector.setter
-    def q_vector(self, new_q_vector):
-        self.k_vector = [(q - 1)/2 for q in new_q_vector]
-
-    @staticmethod
-    def extract_max(string):
-        numbers = re.findall(r'\d+', string)
-        numbers = map(int, numbers)
-        return max(numbers)
-
-    def get_q_vector(self, algebraic=True, lowest_number=2):
-        r"""
-        Returns q-vector with certain properties.
-
-        If slice a specific relation for each cabling-level is preserved.
-        Consider a cable T(2, q_0; 2, q_1; ...;  2, q_n).
-        Then for every q_i, q_(i + 1): q_(i + 1) > q_i * 4
-        """
-        knot_formula = self.knot_formula
-        q_vector = [0] * (self.extract_max(knot_formula) + 1)
-        P = Primes()
-        for layer in self._get_layers_from_formula(knot_formula)[::-1]:
-            for el in layer:
-                q_vector[el] = P.next(lowest_number)
-                lowest_number = q_vector[el]
-            if slice:
-                lowest_number *= 4
-        return q_vector
-
-    @staticmethod
-    def _get_layers_from_formula(knot_formula):
-        r"""helper method for get_q_vector"""
-        k_indices = re.sub(r'[k-]', '', knot_formula)
-        k_indices = re.sub(r'\[\d+\]', lambda x: x.group()[1:-1], k_indices)
-        k_indices = eval(k_indices)
-        number_of_layers = max(len(lst) for lst in k_indices)
-        layers = []
-        for i in range(1, number_of_layers + 1):
-            layer = [lst[-i] for lst in k_indices if len(lst)>= i]
-            layers.append(layer)
-        return layers
-
-    def add_with_shift(self, other):
-        shift = self.extract_max(self.knot_formula) + 1
-        o_formula = re.sub(r'\d+', lambda x: str(int(x.group()) + shift),
-                           other.knot_formula)
-        return self + CableTemplate(o_formula)
-
-    def __add__(self, other):
-        knot_formula = self.knot_formula[:-1] + ",\n" + other.knot_formula[1:]
-        return CableTemplate(knot_formula)
-
-
-
-
-CableSum.get_signature_as_function_of_theta.__doc__ = \
-    """
-    Function intended to construct signature function for a connected
-    sum of multiple cables with varying theta parameter values.
-    Accept arbitrary number of arguments (depending on number of cables in
-    connected sum).
-    Each argument should be given as list of integer representing
-    k - parameters for a cable: parameters k_i (i=1,.., n-1) for satelit knots
-    T(2, 2k_i + 1) and - the last one - k_n for a pattern knot T(2, 2k_n + 1).
-    Returns a function that will take theta vector as an argument and return
-    an object sg.SignatureFunction.
-
-    To calculate signature function for a cable sum and a theta values vector,
-    use as below.
-
-    sage: signature_function_generator = get_signature_as_function_of_theta(
-                                             [1, 3], [2], [-1, -2], [-3])
-    sage: sf = signature_function_generator(2, 1, 2, 2)
-    sage: print(sf)
-    0: 0
-    5/42: 1
-    1/7: 0
-    1/5: -1
-    7/30: -1
-    2/5: 1
-    3/7: 0
-    13/30: -1
-    19/42: -1
-    23/42: 1
-    17/30: 1
-    4/7: 0
-    3/5: -1
-    23/30: 1
-    4/5: 1
-    6/7: 0
-    37/42: -1
-
-    Or like below.
-    sage: print(get_signature_as_function_of_theta([1, 3], [2], [-1, -2], [-3]
-                                                )(2, 1, 2, 2))
-    0: 0
-    1/7: 0
-    1/6: 0
-    1/5: -1
-    2/5: 1
-    3/7: 0
-    1/2: 0
-    4/7: 0
-    3/5: -1
-    4/5: 1
-    5/6: 0
-    6/7: 0
-    """
-
-get_summand_signture_function_docsting = \
-    """
-    This function returns sg.SignatureFunction for previously defined single
-    cable T_(2, q) and a theta given as an argument.
-    The cable was defined by calling function
-    get_summand_signature_as_theta_function(*arg)
-    with the cable description as an argument.
-    It is an implementaion of the formula:
-        Bl_theta(K'_(2, d)) =
-            Bl_theta(T_2, d) + Bl(K')(ksi_l^(-theta) * t)
-            + Bl(K')(ksi_l^theta * t)
-    """
-
-signature_as_function_of_theta_docstring = \
-    """
-    Arguments:
-
-    Returns object of sg.SignatureFunction class for a previously defined
-    connected sum of len(arg) cables.
-    Accept len(arg) arguments: for each cable one theta parameter.
-    If call with no arguments, all theta parameters are set to be 0.
-    """
-#
-# CableSummand.get_blanchfield_for_pattern.__doc__ = \
-#     """
-#     Arguments:
-#         k_n:    a number s.t. q_n = 2 * k_n + 1, where
-#                 T(2, q_n) is a pattern knot for a single cable from a cable sum
-#         theta:  twist/character for the cable (value form v vector)
-#     Return:
-#         sg.SignatureFunction created for pattern signature function
-#         for a given cable and theta/character
-#     Based on:
-#         Proposition 9.8. in Twisted Blanchfield Pairing
-#         (https://arxiv.org/pdf/1809.08791.pdf)
-#     """
-
-# CableSummand.get_summand_signature_as_theta_function.__doc__ = \
-#     """
-#     Argument:
-#         n integers that encode a single cable, i.e.
-#         values of q_i for T(2,q_0; 2,q_1; ... 2, q_n)
-#     Return:
-#         a function that returns sg.SignatureFunction for this single cable
-#         and a theta given as an argument
-#     """

gaknot/clean.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-rm cable_signature.py
-rm signature.py
-rm main.py

gaknot/main.sage

@@ -1,325 +0,0 @@
-#!/usr/bin/env sage -python
-
-
-# TBD
-# print scheme and knot nicely
-# read about Factory Method, variable in docstring, sage documentation,
-# print calc. to output file
-# decide about printing option
-# make __main__?
-
-import os
-import sys
-
-import itertools as it
-import re
-import numpy as np
-import importlib
-
-# constants - which invariants should be calculate
-SIGMA = 0
-SIGNATURE = 1
-
-if __name__ == '__main__':
-    from utility import import_sage
-    package = None
-    path = ''
-
-else:
-    from .utility import import_sage
-    package = os.path.join( __name__.split('.')[0])
-    path = '../'
-sg = import_sage('signature', package=package, path=path)
-cs = import_sage('cable_signature', package=package, path=path)
-
-
-
-
-# class Config:
-#     def __init__(self):
-#         self.f_results = os.path.join(os.getcwd(), "results.out")
-
-class Schema:
-    r"""This class stores interesting schema of cable sums.
-
-    Cable knots sum can be given as a scheme, e.g. a scheme from the paper:
-    K(p_1 , p_2 , q_1 , q_2 , q_3 ) =
-        T(2, q_1; 2, p_1) # -T(2, q_2; 2, p_1) # T(2, p_1) # -T(2, q_3; 2, p_1) +
-        T(2, q_2; 2, p_2) # -T(2, p_2) # T(2, q_3; 2, p_2) # -T(2, q_1; 2, p_2).
-    We can represent it as nested list:
-    lemma_scheme = "[[ k[5],  k[3]], " + \
-                   "[ -k[1], -k[3]], " + \
-                   "[         k[3]], " + \
-                   "[ -k[6], -k[3]], " + \
-                   "[  k[1],  k[7]], " + \
-                   "[        -k[7]], " + \
-                   "[  k[6],  k[7]], " + \
-                   "[ -k[5], -k[7]]]",
-    where each k[i] corresponds to some q_i or p_i.
-    This expression will be later evaluated with k_vector.
-    See k_vector setter in class CableTemplate in cable_signature.sage module.
-
-    Remark 1
-        In the paper, we used p_i and q_i to describe torus knots and cables.
-        It was convenient for writing, but in all the code and documentation
-        only 'q' letter is used to encode torus knots or cables.
-
-    Remark 2
-        There are two ways to set k[i] values for a scheme:
-        via q_vector or k_vector.
-        Both should be lists and the relation is q[i] = 2 * k[i] + 1,
-        i.e. q should be an odd prime and k should be an even number such that
-        2 * k + 1 is prime.
-        To fill the scheme listed above we should use a list of length 8,
-        and k[0] will be omitted as it is not used in the scheme.
-
-    Remark 3
-        Except for development purposes, q_vector was computed with
-        a method CableTemplate.get_q_vector and flag slice=True.
-        The reason for that is that we were interested only in cases
-        where a specific relation for each cabling level is preserved.
-        Consider a cable T(2, q_0; 2, q_1; ...;  2, q_n).
-        Then for every q_i, q_(i + 1): q_(i + 1) > q_i * 4.
-
-    """
-
-    # scheme that is used in the paper
-    lemma_scheme_a = "[ [k[5],  k[3]], " + \
-                     "[ -k[1], -k[3]], " + \
-                     "[         k[3]], " + \
-                     "[ -k[6], -k[3]]]"
-
-    lemma_scheme_b = "[[ k[1],  k[7]], " + \
-                     "[        -k[7]], " + \
-                     "[  k[6],  k[7]], " + \
-                     "[ -k[5], -k[7]]]"
-
-    lemma_scheme = "[[ k[5],  k[3]], " + \
-                   "[ -k[1], -k[3]], " + \
-                   "[         k[3]], " + \
-                   "[ -k[6], -k[3]], " + \
-                   "[  k[1],  k[7]], " + \
-                   "[        -k[7]], " + \
-                   "[  k[6],  k[7]], " + \
-                   "[ -k[5], -k[7]]]"
-
-    #
-    # formula_long = "[[k[0],  k[5],  k[3]], " + \
-    #                "[       -k[5], -k[3]], " + \
-    #                "[        k[2],  k[3]], " + \
-    #                "[-k[4], -k[2], -k[3]]" + \
-    #                "[ k[4],  k[1],  k[7]], " + \
-    #                "[       -k[1], -k[7]], " + \
-    #                "[        k[6],  k[7]], " + \
-    #                "[-k[0], -k[6], -k[7]]]"
-    #
-    # formula_a = "[[k[0],  k[5],  k[3]], " + \
-    #             "[       -k[1], -k[3]], " + \
-    #             "[               k[3]], " + \
-    #             "[-k[4], -k[6], -k[3]]]"
-    #
-    # formula_b = "[[k[4],  k[1],  k[7]], " + \
-    #             "[              -k[7]], " + \
-    #             "[        k[6],  k[7]], " + \
-    #             "[-k[0], -k[5],  -k[7]]]"
-    #
-    # formula_a = "[[ k[0],  k[5],  k[3]], " + \
-    #             "[        -k[1], -k[3]], " + \
-    #             "[         k[2],  k[3]], " + \
-    #             "[ -k[0], -k[2], -k[3]]]"
-    #
-    # formula_b = "[[ k[4],  k[1],  k[7]], " + \
-    #             "[        -k[5], -k[7]], " + \
-    #             "[         k[6],  k[7]], " + \
-    #             "[ -k[4], -k[6], -k[7]]]"
-    #
-    # formula_a = "[[ k[0], k[5],  k[3]], " + \
-    #             "[       -k[5], -k[3]], " + \
-    #             "[        k[2],  k[3]], " + \
-    #             "[-k[4], -k[2], -k[3]]]"
-    #
-    # formula_b = "[[ k[4], k[1],  k[7]], " + \
-    #             "[       -k[1], -k[7]], " + \
-    #             "[        k[6],  k[7]], " + \
-    #             "[-k[0], -k[6], -k[7]]]"
-    #
-    #
-    # three_layers_formula_a = "[[k[0],  k[1],  k[2]],\
-    #                           [        k[3],  k[4]],\
-    #                           [-k[0], -k[3], -k[4]],\
-    #                           [       -k[1], -k[2]]]"
-    #
-    # three_layers_formula_b = "[[k[0],   k[1],  k[2]],\
-    #                           [               k[3]],\
-    #                           [-k[0], -k[1], -k[3]],\
-    #                           [              -k[2]]]"
-    #
-    # short_3_layers_b = "[[         k[5],  k[3]], " + \
-    #                     "[        -k[1], -k[3]], " + \
-    #                     "[                k[3]], " + \
-    #                     "[ -k[4], -k[6], -k[3]]]"
-    #
-    # short_3_layers_b = "[[k[4],   k[1],  k[7]], " + \
-    #                     "[               -k[7]], " + \
-    #                     "[         k[6],  k[7]], " + \
-    #                     "[         -k[5], -k[7]]]"
-    #
-    # four_summands_scheme = "[[ k[0],  k[1],  k[3]]," + \
-    #                        "[        -k[1], -k[3]]," + \
-    #                        "[         k[2],  k[3]]," + \
-    #                        "[ -k[0], -k[2], -k[3]]]"
-    #
-    # two_summands_scheme = "[ [k[0], k[1], k[4]], [-k[1], -k[3]],\
-    #                        [k[2], k[3]], [-k[0], -k[2], -k[4]] ]"
-    # two_small_summands_scheme = "[[k[3]], [-k[3]],\
-    #                             [k[3]], [-k[3]] ]"
-
-
-def main(arg=None):
-    try:
-        limit = int(arg[1])
-    except (IndexError, TypeError):
-        limit = None
-    conf = Config()
-    cable_loop_with_details(conf)
-
-def prove_lemma(verbose=True, details=False):
-
-    if verbose:
-        msg = "CALCULATIONS OF THE SIGMA INVARIANT\n"
-        msg += "Proof of main lemma from "
-        msg += "ON THE SLICE GENUS OF GENERALIZED ALGEBRAIC KNOTS\n\n"
-        print(msg)
-
-    lemma_scheme = Schema.lemma_scheme
-
-    cable_template = cs.CableTemplate(knot_formula=lemma_scheme,
-                                      verbose=verbose)
-    cable_template.fill_q_vector()
-    q_v = cable_template.q_vector
-    cable = cable_template.cable
-    if verbose:
-        msg = "Let us consider a cable knot: \nK =  "
-        msg += cable.knot_description + ".\n"
-        msg += "It is an example of cable knots of a scheme:\n"
-        msg += str(cable_template) + "."
-        print(msg)
-
-    cable.is_function_big_for_all_metabolizers(invariant=SIGMA,
-                                               verbose=verbose,
-                                               details=details)
-
-
-def print_sigma_for_cable(verbose=True):
-
-    lemma_scheme_a = Schema.lemma_scheme_a
-    lemma_scheme_b = Schema.lemma_scheme_b
-    lemma_scheme = Schema.lemma_scheme
-    scheme_four = Schema.four_summands_scheme
-
-    cable_template = cs.CableTemplate(knot_formula=lemma_scheme)
-    cable_template.fill_q_vector()
-    q_v = cable_template.q_vector
-    print(q_v)
-    print(cable_template.cable.knot_description)
-    cable_a = cs.CableTemplate(knot_formula=lemma_scheme_a,
-                              verbose=verbose,
-                              q_vector=q_v
-                             ).cable
-    cable_b = cs.CableTemplate(knot_formula=lemma_scheme_b,
-                              verbose=verbose,
-                              q_vector=q_v
-                             ).cable
-    cable = cs.CableTemplate(knot_formula=lemma_scheme_a,
-                              verbose=verbose,
-                              q_vector=q_v
-                             ).cable
-
-    cable.plot_sigma_for_summands()
-    # cable_a.plot_sigma_for_summands()
-    # cable_b.plot_sigma_for_summands()
-
-
-def cable_loop_with_details(verbose=True):
-    # verbose = False
-    lemma_scheme_a = Schema.lemma_scheme_a
-    lemma_scheme_b = Schema.lemma_scheme_b
-    lemma_scheme = Schema.lemma_scheme
-    cable_template = cs.CableTemplate(knot_formula=lemma_scheme)
-
-    list_of_q_vectors = []
-    # for el in [2, 3, 5, 7, 11, 13]:
-    for el in [2]:
-        cable_template.fill_q_vector(lowest_number=el)
-        q_v = cable_template.q_vector
-        print(q_v)
-        print(cable_template.cable.knot_description)
-        cable_a = cs.CableTemplate(knot_formula=lemma_scheme_a,
-                                  verbose=verbose,
-                                  q_vector=q_v
-                                 ).cable
-        cable_b = cs.CableTemplate(knot_formula=lemma_scheme_b,
-                                  verbose=verbose,
-                                  q_vector=q_v
-                                 ).cable
-    #     print("\n")
-    #     print(cable_a.knot_description)
-        is_a = cable_a.is_function_big_for_all_metabolizers(invariant=cs.SIGMA,
-                                                            verbose=True,
-                                                            details=True)
-        is_b = cable_b.is_function_big_for_all_metabolizers(invariant=cs.SIGMA,
-                                                            verbose=True,
-                                                            details=True)
-        if is_a and is_b:
-            print("sigma is big for all metabolizers")
-        else:
-            print("sigma is not big for all metabolizers")
-        print("\n" * 3)
-
-
-def few_cable_without_calc(verbose=False):
-
-    lemma_scheme_a = Schema.lemma_scheme_a
-    lemma_scheme_b = Schema.lemma_scheme_b
-    lemma_scheme = Schema.lemma_scheme
-
-    cable_template = cs.CableTemplate(knot_formula=lemma_scheme)
-
-    list_of_q_vectors = []
-    for el in [2, 3, 5, 7, 11, 13]:
-        cable_template.fill_q_vector(lowest_number=el)
-        q_v = cable_template.q_vector
-        print(q_v)
-        print(cable_template.cable.knot_description)
-        cable_a = cs.CableTemplate(knot_formula=lemma_scheme_a,
-                              verbose=verbose,
-                              q_vector=q_v
-                             ).cable
-        cable_b = cs.CableTemplate(knot_formula=lemma_scheme_b,
-                                  verbose=verbose,
-                                  q_vector=q_v
-                                 ).cable
-        is_a = cable_a.is_function_big_for_all_metabolizers(invariant=sigma)
-        is_b = cable_b.is_function_big_for_all_metabolizers(invariant=sigma)
-        if is_a and is_b:
-            print("sigma is big for all metabolizers")
-        else:
-            print("sigma is not big for all metabolizers")
-        print("\n" * 3)
-
-
-def plot_many_untwisted_signature_functions(range_tuple=(1, 10)):
-    P = Primes()
-    for i in range(*range_tuple):
-        q = P.unrank(i)
-        a = cs.CableSummand.get_untwisted_signature_function(q=q)
-        a.plot()
-
-
-if __name__ == '__main__':
-    if '__file__' in globals():
-        # skiped in interactive mode as __file__ is not defined
-        main(sys.argv)
-    else:
-        pass
-        # main()

gaknot/utility.py

@@ -1,90 +0,0 @@
-import importlib
-import os
-import sys
-import re
-import math
-import logging
-
-def mod_one(n):
-    r"""calculates the fractional part of the argument
-
-    Argument:
-        a number
-    Return:
-        the fractional part of the argument
-    Examples:
-        sage: mod_one(9 + 3/4)
-        3/4
-        sage: mod_one(-9 + 3/4)
-        3/4
-        sage: mod_one(-3/4)
-        1/4
-    """
-    return n - math.floor(n)
-
-
-def import_sage(module_name, package=None, path=''):
-    r"""Import or reload SageMath modules with preparse if the sage file exist.
-
-    Arguments:
-        module_name - name of the module (without file extension!)
-        package - use only if module is used as a part of a package
-    Return:
-        module
-    Examples:
-
-        from utility import import_sage
-
-        # equivalent to import module_name as my_prefered_shortcut}
-        my_prefered_shortcut = import_sage('module_name')
-    """
-    sage_name = module_name + ".sage"
-    python_name = module_name + ".sage.py"
-
-    logging.info("\n\nimport_sage called with arguments:" +
-                 "\n\tmodule_name: " + module_name +
-                 "\n\tpackage: " + str(package) +
-                 "\n\tpath: " + path)
-
-
-
-    if package is not None:
-
-        path_from_package_name = re.sub(r'\.', r'\\', package)
-        path = os.path.join(path, path_from_package_name)
-
-        logging.info("path with package name: " + str(path))
-
-
-    sage_path = os.path.join(path, sage_name)
-    python_path = os.path.join(path, python_name)
-    module_path = os.path.join(path, module_name)
-
-    if os.path.isfile(sage_path):
-        logging.info("\nPreparsing sage file " + sage_name + ".")
-        os.system('sage --preparse {}'.format(sage_path));
-        os.system('mv {} {}.py'.format(python_path, module_path))
-    else:
-        logging.info("sage file not found: " + str(sage_path))
-
-
-
-    if package is not None:
-        module_name = package + "." + module_name
-
-    if module_name in sys.modules:
-        logging.info("\nmodule " + module_name + " was found.")
-        return importlib.reload(sys.modules[module_name])
-    return importlib.import_module(module_name, package=package)
-
-
-def parse_sage(module_name):
-
-    dir = os.path.dirname(__file__)
-
-    sage_name = os.path.join(dir, module_name + ".sage")
-    python_name = os.path.join(dir, module_name + ".sage.py")
-    module_name = os.path.join(dir, module_name + ".py")
-
-    os.system('sage --preparse {}'.format(sage_name))
-    os.system('mv {} {}'.format(python_name, module_name))

main.sage

@@ -0,0 +1,173 @@
+#!/usr/bin/python
+
+# TBD: read about Factory Method, variable in docstring, sage documentation,
+# print calc. to output file
+# delete separation for twisted_part and untwisted_part
+# decide about printing option
+
+import os
+import sys
+
+import itertools as it
+import re
+import numpy as np
+
+attach("signature.sage")
+attach("cable_signature.sage")
+
+
+
+
+class Config(object):
+    def __init__(self):
+        self.f_results = os.path.join(os.getcwd(), "results.out")
+
+        # knot_formula is a schema for knots which signature function
+        # will be calculated
+        self.knot_formula = "[[k[0], k[1], k[3]], " + \
+                             "[-k[1], -k[3]], " + \
+                             "[k[2], k[3]], " + \
+                             "[-k[0], -k[2], -k[3]]]"
+
+        # self.knot_formula = "[[k[0], k[1], k[4]], [-k[1], -k[3]], \
+        #                      [k[2], k[3]], [-k[0], -k[2], -k[4]]]"
+        #
+        # self.knot_formula = "[[k[3]], [-k[3]], \
+        #                      [k[3]], [-k[3]] ]"
+        #
+        # self.knot_formula = "[[k[3], k[2], k[0]], [-k[2], -k[0]], \
+        #                      [k[1], k[0]], [-k[3], -k[1], -k[0]]]"
+        #
+        # self.knot_formula = "[[k[0], k[1], k[2]], [k[3], k[4]], \
+        #                      [-k[0], -k[3], -k[4]], [-k[1], -k[2]]]"
+        # self.knot_formula = "[[k[0], k[1], k[2]], [k[3]],\
+        #                          [-k[0], -k[1], -k[3]], [-k[2]]]"
+        self.limit = 3
+
+        self.verbose = True
+        # self.verbose = False
+
+
+
+def main(arg=None):
+    try:
+        limit = int(arg[1])
+    except (IndexError, TypeError):
+        limit = None
+
+    # global cable_template , cable_template_2, cable_template_1
+
+    knot_formula = "[[k[0], k[1], k[3]], " + \
+                     "[-k[1], -k[3]], " + \
+                     "[k[2], k[3]], " + \
+                     "[-k[0], -k[2], -k[3]]]"
+    template = CableTemplate(knot_formula, q_vector=[3, 5, 7, 11])
+    cab = template.cable
+    # cab.plot_all_summands()
+    cab.plot_sum_for_theta_vector([0,4,0,4], save_to_dir=True)
+    # knot_formula = config.knot_formula
+    # q_vector = (3, 5, 7, 13)
+    # q_vector = (3, 5, 7, 11)
+    return
+
+    formula_1 = "[[k[0], k[5], k[3]], " + \
+                      "[-k[1], -k[3]], " + \
+                       "[k[2], k[3]], " + \
+               "[-k[0], -k[2], -k[3]]]"
+    formula_2 = "[[k[4], k[1], k[7]], " + \
+                      "[-k[5], -k[7]], " + \
+                       "[k[6], k[7]], " + \
+               "[-k[4], -k[6], -k[7]]]"
+    q_vector = (5, 13, 19, 41,\
+                7, 17, 23, 43)
+    q_vector_small = (3, 7, 13, 19,\
+                5, 11, 17, 23)
+
+    cable_template_1 = CableTemplate(knot_formula=formula_1)
+    cable_template_2 = CableTemplate(knot_formula=formula_2)
+    cable_template = cable_template_1 + cable_template_2
+    cable_with_shift = cable_template_1.add_with_shift(cable_template_2)
+    print(cable_with_shift.knot_formula)
+    cable_template.fill_q_vector()
+    cable = cable_template.cable
+
+    sf = cable(4,4,4,4,0,0,0,0)
+    writer = SignatureWriter(sf)
+    writer.plot(title="hoho")
+
+    sf = cable_template.cable.signature_as_function_of_theta(4,1,1,4,0,0,0,0)
+    writer = SignatureWriter(sf)
+    writer.plot(title="hoho", color='red')
+
+
+    cable_template.cable.is_signature_big_for_all_metabolizers()
+
+
+    cable_template_1 = CableTemplate(knot_formula=formula_1)
+    cable_template_2 = CableTemplate(knot_formula=formula_2)
+    cable_template = cable_template_1 + cable_template_2
+    cable_template.cable.is_signature_big_for_all_metabolizers()
+    sf = cable_template.cable.signature_as_function_of_theta(4,4,4,4,0,0,0,0)
+    writer = SignatureWriter(sf)
+    writer.plot(title="hoho")
+
+
+
+
+
+
+
+
+
+if __name__ == '__main__':
+    global config
+    config = Config()
+    if '__file__' in globals():
+        # skiped in interactive mode as __file__ is not defined
+        main(sys.argv)
+    else:
+        pass
+        # main()
+
+
+"""
+This script calculates signature functions for knots (cable sums).
+
+The script can be run as a sage script from the terminal
+or used in interactive mode.
+
+A knot (cable sum) is encoded as a list where each element (also a list)
+corresponds to a cable knot, e.g. a list
+[[1, 3], [2], [-1, -2], [-3]] encodes
+T(2, 3; 2, 7) # T(2, 5) # -T(2, 3; 2, 5) # -T(2, 7).
+
+To calculate the number of characters for which signature function vanish use
+the function eval_cable_for_null_signature as shown below.
+
+sage: eval_cable_for_null_signature([[1, 3], [2], [-1, -2], [-3]])
+
+T(2, 3; 2, 7) # T(2, 5) # -T(2, 3; 2, 5) # -T(2, 7)
+Zero cases: 1
+All cases: 1225
+Zero theta combinations:
+(0, 0, 0, 0)
+
+sage:
+
+The numbers given to the function eval_cable_for_null_signature are k-values
+for each component/cable in a direct sum.
+
+To calculate signature function for a knot and a theta value, use function
+get_signature_as_function_of_theta (see help/docstring for details).
+
+About notation:
+Cables that we work with follow a schema:
+    T(2, q_1; 2, q_2; 2, q_4) # -T(2, q_2; 2, q_4) #
+            # T(2, q_3; 2, q_4) # -T(2, q_1; 2, q_3; 2, q_4)
+In knot_formula each k[i] is related with some q_i value, where
+q_i = 2*k[i] + 1.
+So we can work in the following steps:
+1) choose a schema/formula by changing the value of knot_formula
+2) set each q_i all or choose range in which q_i should varry
+3) choose vector v / theata vector.
+"""

notebooks/lemma.ipynb

@@ -1,99 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import path\n",
-    "import logging\n",
-    "from contextlib import redirect_stdout\n",
-    "# logging.basicConfig(level=logging.INFO)\n",
-    "import gaknot"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Lemma "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "gaknot.prove_lemma()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Details to file"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with open('very_detailed_calculations.txt', 'w') as f:\n",
-    "    with redirect_stdout(f):\n",
-    "        gaknot.prove_lemma(details=True)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Calculations to file"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with open('calculations.txt', 'w') as f:\n",
-    "    with redirect_stdout(f):\n",
-    "        gaknot.prove_lemma(details=False)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "SageMath 9.0",
-   "language": "sage",
-   "name": "sagemath"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

notebooks/path.py

@@ -1,8 +0,0 @@
-#!/usr/bin/env python3
-
-import sys
-import os
-
-module_path = os.path.abspath(os.pardir)
-if module_path not in sys.path:
-    sys.path.append(module_path)

notebooks/tests.ipynb

@@ -1,580 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%matplotlib inline\n",
-    "%load_ext pycodestyle_magic\n",
-    "\n",
-    "# display full output, not only last result, except ended with semicolon\n",
-    "from IPython.core.interactiveshell import InteractiveShell\n",
-    "InteractiveShell.ast_node_interactivity = 'all';\n",
-    "from IPython.display import Image, SVG\n",
-    "import logging\n",
-    "logging.basicConfig(level=logging.INFO)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import path\n",
-    "from gaknot import import_sage\n",
-    "cs = import_sage('cable_signature', package='gaknot', path=path.module_path)\n",
-    "sg = import_sage('signature', package='gaknot', path=path.module_path)\n",
-    "m = import_sage('main', package='gaknot', path=path.module_path)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "m.prove_lemma(verbose=True)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Other cables"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "# knot_formula = \"[[k[0], k[1], k[3]],\" + \\\n",
-    "#                \" [-k[1], -k[3]],\" + \\\n",
-    "#                \" [k[2], k[3]],\" + \\\n",
-    "#                \" [-k[0], -k[2], -k[3]]]\"\n",
-    "# # q_vector = (3, 5, 7, 13)\n",
-    "# q_vector = (3, 5, 7, 11)\n",
-    "\n",
-    "# template = cs.CableTemplate(knot_formula, q_vector=q_vector, verbose=True)\n",
-    "# cable = template.cable\n",
-    "# # cable.plot_all_summands()\n",
-    "# cable.is_function_big_for_all_metabolizers(invariant=cs.SIGMA)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Cables with 8 direct summands "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "formula_1 = \"[[k[0], k[5], k[3]], \" + \\\n",
-    "                  \"[-k[1], -k[3]], \" + \\\n",
-    "                   \"[k[2], k[3]], \" + \\\n",
-    "           \"[-k[0], -k[2], -k[3]]]\"\n",
-    "formula_2 = \"[[k[4], k[1], k[7]], \" + \\\n",
-    "                  \"[-k[5], -k[7]], \" + \\\n",
-    "                   \"[k[6], k[7]], \" + \\\n",
-    "           \"[-k[4], -k[6], -k[7]]]\"\n",
-    "\n",
-    "\n",
-    "\n",
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cable_template.knot_formula"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Relatively small cables "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# q_vector = (5, 13, 19, 41,\\\n",
-    "#             7, 17, 23, 43)\n",
-    "# cable_template.fill_q_vector(q_vector=q_vector)\n",
-    "# cable = cable_template.cable\n",
-    "# print(cable.knot_description)\n",
-    "\n",
-    "# q_vector_small = (3, 7, 13, 19,\\\n",
-    "#                   5, 11, 17, 23)\n",
-    "# cable_template.fill_q_vector(q_vector=q_vector)\n",
-    "# cable = cable_template.cable\n",
-    "# print(cable.knot_description)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# cable.is_signature_big_for_all_metabolizers()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Slice candidate"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "# cable_template.fill_q_vector()\n",
-    "# # print(cable_template.q_vector)\n",
-    "# # print(cable_template.knot_formula)\n",
-    "\n",
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "# sf = slice_canidate(4,4,4,4,0,0,0,0)\n",
-    "# sf = slice_canidate(4,1,1,4,0,0,0,0)\n",
-    "\n",
-    "\n",
-    "# cable.is_signature_big_for_all_metabolizers()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "\n",
-    "# knot_formula = \"[[k[0], k[1], k[4]], [-k[1], -k[3]],\\\n",
-    "#                  [k[2], k[3]], [-k[0], -k[2], -k[4]]]\"\n",
-    "\n",
-    "# knot_formula = \"[[k[3]], [-k[3]],\\\n",
-    "#                 [k[3]], [-k[3]] ]\"\n",
-    "\n",
-    "# knot_formula = \"[[k[3], k[2], k[0]], [-k[2], -k[0]],\\\n",
-    "#                  [k[1], k[0]], [-k[3], -k[1], -k[0]]]\"\n",
-    "\n",
-    "# knot_formula = \"[[k[0], k[1], k[2]], [k[3], k[4]],\\\n",
-    "#                  [-k[0], -k[3], -k[4]], [-k[1], -k[2]]]\"\n",
-    "\n",
-    "# knot_formula = \"[[k[0], k[1], k[2]], [k[3]],\\\n",
-    "#                  [-k[0], -k[1], -k[3]], [-k[2]]]\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "formula_1 = \"[[k[0], k[5], k[3]], \" + \\\n",
-    "                  \"[-k[1], -k[3]], \" + \\\n",
-    "                   \"[k[2], k[3]], \" + \\\n",
-    "           \"[-k[0], -k[2], -k[3]]]\"\n",
-    "formula_2 = \"[[k[4], k[1], k[7]], \" + \\\n",
-    "                  \"[-k[5], -k[7]], \" + \\\n",
-    "                   \"[k[6], k[7]], \" + \\\n",
-    "           \"[-k[4], -k[6], -k[7]]]\"\n",
-    "\n",
-    "\n",
-    "\n",
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2\n",
-    "\n",
-    "# cable_template.fill_q_vector()\n",
-    "# # print(cable_template.q_vector)\n",
-    "# # print(cable_template.knot_formula)\n",
-    "\n",
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "# sf = slice_canidate(4,4,4,4,0,0,0,0)\n",
-    "# sf = slice_canidate(4,1,1,4,0,0,0,0)\n",
-    "\n",
-    "\n",
-    "# slice_canidate.q_order\n",
-    "# # slice_canidate.is_signature_big_for_all_metabolizers()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "formula_1 = \"[[k[0], k[5], k[3]], \" + \\\n",
-    "                  \"[-k[5], -k[3]], \" + \\\n",
-    "                   \"[k[2], k[3]], \" + \\\n",
-    "            \"[-k[4], -k[2], -k[3]]]\"\n",
-    "formula_2 = \"[[k[4], k[1], k[7]], \" + \\\n",
-    "                  \"[-k[1], -k[7]], \" + \\\n",
-    "                   \"[k[6], k[7]], \" + \\\n",
-    "            \"[-k[0], -k[6], -k[7]]]\"\n",
-    "\n",
-    "\n",
-    "\n",
-    "\n",
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2\n",
-    "# cable_template.fill_q_vector()\n",
-    "\n",
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "\n",
-    "# slice_canidate.q_order\n",
-    "# # slice_canidate.is_signature_big_for_all_metabolizers()\n",
-    "# sigma = slice_canidate.get_sigma_as_function_of_theta()\n",
-    "# # sigma((0, 6, 6, 0, 0,0,0,0))\n",
-    "# # 13450/83\n",
-    "# sigma((9, 9, 9, 9, 0,0,0,0))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "\n",
-    "\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "formula_1 = \"[[k[0], k[5], k[3]], \" + \\\n",
-    "                  \"[-k[1], -k[3]], \" + \\\n",
-    "                         \"[ k[3]], \" + \\\n",
-    "            \"[-k[4], -k[6], -k[3]]]\"\n",
-    "\n",
-    "formula_2 = \"[[k[4], k[1], k[7]], \" + \\\n",
-    "                       \"[ -k[7]], \" + \\\n",
-    "                   \"[k[6], k[7]], \" + \\\n",
-    "            \"[-k[0], -k[5], -k[7]]]\"\n",
-    "\n",
-    "\n",
-    "\n",
-    "\n",
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2\n",
-    "\n",
-    "# cable_template.fill_q_vector()\n",
-    "# # print(cable_template.q_vector)\n",
-    "# # print(cable_template.knot_formula)\n",
-    "\n",
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "# sf = slice_canidate(4,4,4,4,0,0,0,0)\n",
-    "# sf = slice_canidate(4,1,1,4,0,0,0,0)\n",
-    "# slice_canidate.is_signature_big_for_all_metabolizers()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "formula_1 = \"       [ [k[5],  k[3]], \" + \\\n",
-    "            \"       [ -k[1], -k[3]], \" + \\\n",
-    "                   \"       [  k[3]], \" + \\\n",
-    "            \"[-k[4],  -k[6], -k[3]]]\"\n",
-    "\n",
-    "formula_2 = \"[[k[4],   k[1],  k[7]], \" + \\\n",
-    "                       \"[    -k[7]], \" + \\\n",
-    "                     \"[k[6],  k[7]], \" + \\\n",
-    "                    \"[-k[5], -k[7]]]\"\n",
-    "\n",
-    "\n",
-    "\n",
-    "\n",
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2\n",
-    "\n",
-    "# cable_template.fill_q_vector()\n",
-    "# # print(cable_template.q_vector)\n",
-    "# # print(cable_template.knot_formula)\n",
-    "\n",
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "# sf = slice_canidate(4,4,4,4,0,0,0,0)\n",
-    "# sf = slice_canidate(4,1,1,4,0,0,0,0)\n",
-    "# slice_canidate.q_order\n",
-    "# # slice_canidate.is_signature_big_for_all_metabolizers()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sf = slice_canidate()\n",
-    "# sf = sf[2]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sf.plot()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "formula_1 = \"[ [k[5],  k[3]], \" + \\\n",
-    "            \"[ -k[1], -k[3]], \" + \\\n",
-    "            \"[         k[3]], \" + \\\n",
-    "            \"[ -k[6], -k[3]]]\"\n",
-    "\n",
-    "formula_2 = \"[[ k[1],   k[7]], \" + \\\n",
-    "             \"[        -k[7]], \" + \\\n",
-    "             \"[  k[6],  k[7]], \" + \\\n",
-    "             \"[ -k[5], -k[7]]]\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cable_template_1 = cs.CableTemplate(knot_formula=formula_1)\n",
-    "# cable_template_2 = cs.CableTemplate(knot_formula=formula_2)\n",
-    "# cable_template = cable_template_1 + cable_template_2"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cable_template.knot_formula"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cable_template.fill_q_vector()\n",
-    "# print(cable_template.q_vector)\n",
-    "# print(cable_template.knot_formula)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# cable_template.fill_q_vector()\n",
-    "# print(cable_template.q_vector)\n",
-    "# print(cable_template.knot_formula)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# slice_canidate = cable_template.cable\n",
-    "# print(slice_canidate.knot_description)\n",
-    "# sf = slice_canidate(4,4,4,4,0,0,0,0)\n",
-    "# sf = slice_canidate(4,1,1,4,0,0,0,0)\n",
-    "# slice_canidate.q_order"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# slice_canidate.is_sigma_big_for_all_metabolizers()\n",
-    "# slice_canidate.is_signature_big_for_all_metabolizers()\n",
-    "# slice_canidate.is_function_big_for_all_metabolizers()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# slice_canidate.is_function_big_for_all_metabolizers(invariant=cs.SIGMA)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# slice_canidate.is_function_big_for_all_metabolizers(invariant=cs.SIGNATURE)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sigma = slice_canidate.get_sigma_as_function_of_theta()\n",
-    "# sigma((0, 6, 6, 0, 0,0,0,0))\n",
-    "# # 13450/83\n",
-    "# sigma((9, 0, 0, 9, 0,0,0,0))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# _, _, sf = slice_canidate((1, 1, 0, 0, 0,0,0,0))\n",
-    "# sf"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sg.SignaturePloter.plot(sf)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "\n",
-    "# slice_canidate.plot_sum_for_theta_vector([0r,4r,0r,4r,0r,0r,0r,0r], save_to_dir=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sf.plot()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# help(cs.CableTemplate.get_q_vector)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "SageMath 9.0",
-   "language": "sage",
-   "name": "sagemath"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

signature.sage

@@ -1,51 +1,28 @@
-#!/usr/bin/env sage -python
-
-import sys
-# import os
+#!/usr/bin/python
+import numpy as np
+import itertools as it
+from typing import Iterable
 from collections import Counter
+from sage.arith.functions import LCM_list
+import warnings
+import re
 import matplotlib.pyplot as plt
 import inspect
 from PIL import Image
 from pathlib import Path
-import warnings
-from .utility import mod_one
-
-
-# check if used in Jupyter Notebook to show plots in proper way
-JUPYTER = 'ipykernel'
-IPy_TERMINAL = 'IPython'
-
-def get_ipython_info():
-    if JUPYTER in sys.modules:
-        return JUPYTER
-    elif IPy_TERMINAL in sys.modules:
-        return IPy_TERMINAL
-    return False
-
-global ipython_info
-ipython_info = get_ipython_info()
-
-#
-#
 # 9.11 (9.8)
 # 9.15 (9.9)
 
 
-class SignatureFunction:
-    r"""signature function is entirely encoded by its signature
-    jump, the class stores only information about signature jumps
-    in a dictionary self.jumps_counter
-    The dictionary stores data of the signature jump as a key/values pair,
-    where the key is the argument at which the functions jumps
-    and value encodes the value of the jump. Remember that we treat
-    signature functions as defined on the interval \[0,1).
-    """
-    def __init__(self, values=None, counter=None, plot_title=''):
+class SignatureFunction():
+
+    def __init__(self, values=None, counter=None):
 
         # counter of signature jumps
         if counter is None:
             counter = Counter()
-            values = values or []
+            if values is None:
+                values = []
             for k, v in values:
                 counter[k] += v
 
@@ -57,7 +34,6 @@ class SignatureFunction:
         counter[0] += 0
         counter[1] += 0
         self.jumps_counter = counter
-        self.plot_title = plot_title
 
     def __rshift__(self, shift):
         # A shift of the signature functions corresponds to the rotation.
@@ -76,26 +52,13 @@ class SignatureFunction:
     def __add__(self, other):
         counter = copy(self.jumps_counter)
         counter.update(other.jumps_counter)
-        if self.plot_title and other.plot_title:
-            title = self.plot_title + " + " + other.plot_title
-        else:
-            title = self.plot_title or other.plot_title
-        return SignatureFunction(counter=counter, plot_title=title)
+        return SignatureFunction(counter=counter)
 
     def __sub__(self, other):
         counter = copy(self.jumps_counter)
         counter.subtract(other.jumps_counter)
         return SignatureFunction(counter=counter)
 
-    def __mul__(self, number):
-        # scalar multiplication
-        counter = Counter({k : number * v \
-                          for k, v in self.jumps_counter.items()})
-        return SignatureFunction(counter=counter)
-
-    def __rmul__(self, number):
-        return(self.__mul__(number))
-
     def __eq__(self, other):
         return self.jumps_counter == other.jumps_counter
 
@@ -116,6 +79,9 @@ class SignatureFunction:
         result = [jump for jump_arg, jump in items if jump_arg < mod_one(arg)]
         return 2 * sum(result) + self.jumps_counter[arg]
 
+    def is_zero_everywhere(self):
+        return not any(self.jumps_counter.values())
+
     def double_cover(self):
         # to read values for t^2
         items = self.jumps_counter.items()
@@ -137,74 +103,75 @@ class SignatureFunction:
         counter = Counter({mod_one(2 * k) : v for k, v in items if k >= 1/2})
         return SignatureFunction(counter=counter)
 
-    def is_zero_everywhere(self):
-        return not any(self.jumps_counter.values())
-
-    def extremum(self, limit=math.inf):
-        max_point = (0, 0)
+    def extremum(self, limit=None):
+        max = 0
         current = 0
         items = sorted(self.jumps_counter.items())
         for arg, jump in items:
             current += 2 * jump
             assert current == self(arg) + jump
-            if abs(current) > abs(max_point[1]):
-                max_point  = (arg, current)
-                if abs(current) > limit:
+            if abs(current) > abs(max):
+                max = current
+                if limit is not None:
+                    if abs(max) > limit:
                         break
-        return max_point
+        return max
 
     def total_sign_jump(self):
         # Total signature jump is the sum of all jumps.
         return sum([j[1] for j in sorted(self.jumps_counter.items())])
 
-    def plot(self, *args, **kargs):
-        SignaturePloter.plot(self, *args, **kargs)
+    def plot_four(self, sf1, sf2, sf3, save_path=None, title=''):
 
-
-class SignaturePloter:
-
-    @classmethod
-    def plot_many(cls, *sf_list, save_path=None, title='', cols=None):
-
-        axes_num = len(sf_list)
-        if axes_num > 36:
-            sf_list = sf_list[36]
-            axes_num = 36
-            msg = "To many functions for the plot were given. "
-            msg += "Only 36 can be plotted "
-            warnings.warn(msg)
-
-            # print war, set val in conf
-        cols = cols or ceil(sqrt(axes_num))
-        rows = ceil(axes_num/cols)
-        fig, axes_matrix = plt.subplots(rows, cols,
-                                        sharex='col', sharey='row',
-                                        gridspec_kw={'hspace': 0, 'wspace': 0},
-                                        # sharey=True,
-                                        # sharex=True,
-                                        )
-        for i, sf in enumerate(sf_list):
-            col = i % cols
-            row = (i - col)/cols
+        fig, axes_matrix = plt.subplots(2, 2, sharey=True,
+                                        figsize=(10,5))
+        sf0 = self
         sf.plot(subplot=True,
-                     ax=axes_matrix[row][col],
-                     title=sf.plot_title)
-
-        fig.suptitle(title)
-        plt.tight_layout()
-
-        cls.show_and_save(save_path)
-
-    @classmethod
-    def plot_sum_of_two(cls, sf1, sf2, save_path=None, title=''):
-
-        sf = sf1 + sf2
-        fig, axes_matrix = plt.subplots(2, 2, sharey=True, figsize=(10,5))
-
-        sf1.plot(subplot=True,
                 ax=axes_matrix[0][1])
 
+        sf1.plot(subplot=True,
+                ax=axes_matrix[1][0],
+                color='red',
+                linestyle='dotted')
+
         sf2.plot(subplot=True,
+                ax=axes_matrix[0][0],
+                color='black')
+
+        sf3.plot(subplot=True,
+                ax=axes_matrix[1][1],
+                alpha=0.3)
+
+        fig.suptitle(title)
+
+        plt.tight_layout()
+        if save_path is None:
+            save_path = os.path.join(os.getcwd(),"tmp.png")
+        save_path = Path(save_path)
+        save_path = save_path.with_suffix('.png')
+
+        plt.savefig(save_path)
+        plt.close()
+        image = Image.open(save_path)
+        image.show()
+
+
+        pass
+
+
+    def plot_sum_with_other(self, other,
+                            save_path=None, title=''):
+        tp = self
+        up = other
+        sf = tp + up
+
+        fig, axes_matrix = plt.subplots(2, 2, sharey=True,
+                                        figsize=(10,5))
+
+        tp.plot(subplot=True,
+                ax=axes_matrix[0][1])
+
+        up.plot(subplot=True,
                 ax=axes_matrix[1][0],
                 color='red',
                 linestyle='dotted')
@@ -213,11 +180,11 @@ class SignaturePloter:
                 ax=axes_matrix[0][0],
                 color='black')
 
-        sf1.plot(subplot=True,
+        tp.plot(subplot=True,
                 ax=axes_matrix[1][1],
                 alpha=0.3)
 
-        sf2.plot(subplot=True,
+        up.plot(subplot=True,
                 ax=axes_matrix[1][1],
                 color='red', alpha=0.3,
                 linestyle='dotted')
@@ -228,78 +195,63 @@ class SignaturePloter:
                 alpha=0.7,)
 
         fig.suptitle(title)
+
         plt.tight_layout()
+        if save_path is None:
+            save_path = os.path.join(os.getcwd(),"tmp.png")
+        save_path = Path(save_path)
+        save_path = save_path.with_suffix('.png')
 
-        cls.show_and_save(save_path)
 
-    @classmethod
-    def plot(cls, sf, subplot=False, ax=None,
-             save_path=None,
-             title='',
+        # print(save_as)
+
+        plt.savefig(save_path)
+        plt.close()
+        image = Image.open(save_path)
+        image.show()
+
+
+        pass
+
+
+    def plot(self, subplot=False, ax=None, save_as='sf',
+             title="",
              alpha=1,
              color='blue',
              linestyle='solid',
-             special_point=None,
-             special_label='',
-             extraticks=None,
              ylabel=''):
 
         if ax is None:
             fig, ax = plt.subplots(1, 1)
 
-        keys = sorted(sf.jumps_counter.keys())
-        y = [(sf(k) + sf.jumps_counter[k]) for k in keys[:-1]]
+        keys = sorted(self.jumps_counter.keys())
+        y = [self(k) + self.jumps_counter[k] for k in keys]
         xmax = keys[1:]
         xmin = keys[:-1]
 
         ax.set(ylabel=ylabel)
         ax.set(title=title)
         ax.hlines(y, xmin, xmax, color=color, linestyle=linestyle, alpha=alpha)
-        if special_point is not None:
-            arg, val = special_point
-            extraticks = extraticks or []
-            plt.xticks(list(plt.xticks()[0]) + extraticks)
-            ext = sf.extremum()[1]
-            ytext = ext/2 + 1/2
-            xtext = arg + 1/5
 
-            ax.annotate(special_label, xy=(arg, val), xytext=(xtext, ytext),
-                        arrowprops=dict(facecolor='black', shrink=0.05,
-                                        alpha=0.7, width=2),)
         if subplot:
             return ax
 
-        cls.show_and_save(save_path)
-
-    @staticmethod
-    def show_and_save(save_path):
-
-        if save_path is not None:
-            save_path = Path(save_path)
-            save_path = save_path.with_suffix('.png')
-            plt.savefig(save_path)
-
-        if ipython_info == JUPYTER:
-            plt.show()
-
-        elif True:  # save_path is None:
-            plt.savefig('tmp.png')
+        save_as += ".png"
+        plt.savefig(save_as)
         plt.close()
-            image = Image.open('tmp.png')
+        image = Image.open(save_as)
         image.show()
-            # msg = "For interactive shell set save_path."
-            # warnings.warn(msg)
 
-    @staticmethod
-    def step_function_data(sf):
+
+
+    def step_function_data(self):
         # Transform the signature jump data to a format understandable
         # by the plot function.
-        result = [(k, sf.sf(k) + sf.jumps_counter[k])
-                 for k in sorted(sf.jumps_counter.keys())]
+        result = [(k, self.sf(k) + self.jumps_counter[k])
+                 for k in sorted(self.jumps_counter.keys())]
         return result
 
-    @staticmethod
-    def tikz_plot(sf, save_as):
+    def tikz_plot(self, save_as):
         plt_sin = plot(sin(x), (x, 0, 2*pi))
         # plt_sin.show()
         plt_sin.save("MyPic.pdf")
@@ -374,3 +326,34 @@ class SignaturePloter:
                 \end{document}
                 """
             f.write(tail)
+
+def mod_one(n):
+    return n - floor(n)
+
+SignatureFunction.__doc__ = \
+    """
+    This simple class encodes twisted and untwisted signature functions
+    of knots. Since the signature function is entirely encoded by its signature
+    jump, the class stores only information about signature jumps
+    in a dictionary self.jumps_counter.
+    The dictionary stores data of the signature jump as a key/values pair,
+    where the key is the argument at which the functions jumps
+    and value encodes the value of the jump. Remember that we treat
+    signature functions as defined on the interval [0,1).
+    """
+
+
+mod_one.__doc__ = \
+    """
+    Argument:
+        a number
+    Return:
+        the fractional part of the argument
+    Examples:
+        sage: mod_one(9 + 3/4)
+        3/4
+        sage: mod_one(-9 + 3/4)
+        3/4
+        sage: mod_one(-3/4)
+        1/4
+    """