Source code for tsfresh.examples.driftbif_simulation

# -*- coding: utf-8 -*-
# This file as well as the whole tsfresh package are licenced under the MIT licence (see the LICENCE.txt)
# Maximilian Christ (, Blue Yonder Gmbh, 2016

# Thanks to Andreas W. Kempa-Liehr for providing this snippet

import logging

import numpy as np
import pandas as pd

_logger = logging.getLogger(__name__)

[docs]class velocity: """ Simulates the velocity of a dissipative soliton (kind of self organized particle) [6]_. The equilibrium velocity without noise R=0 for $\tau>1.0/\\kappa_3$ is $\\kappa_3 \\sqrt{(tau - 1.0/\\kappa_3)/Q}. Before the drift-bifurcation $\tau \\le 1.0/\\kappa_3$ the velocity is zero. References ---------- .. [6] Andreas Kempa-Liehr (2013, p. 159-170) Dynamics of Dissipative Soliton Dissipative Solitons in Reaction Diffusion Systems. Springer: Berlin >>> ds = velocity(tau=3.5) # Dissipative soliton with equilibrium velocity 1.5e-3 >>> print(ds.label) # Discriminating before or beyond Drift-Bifurcation 1 # Equilibrium velocity >>> print(ds.deterministic) 0.0015191090506254991 # Simulated velocity as a time series with 20000 time steps being disturbed by Gaussian white noise >>> v = ds.simulate(20000) """ def __init__(self, tau=3.8, kappa_3=0.3, Q=1950.0, R=3e-4, delta_t=0.05, seed=None): """ :param tau: Bifurcation parameter determining the intrinsic velocity of the dissipative soliton, which is zero for tau<=1.0/kappa_3 and np.sqrt(kappa_3**3/Q * (tau - 1.0/kappa_3)) otherwise :type tau: float :param kappa_3: Inverse bifurcation point. :type kappa_3: :param Q: Shape parameter of dissipative soliton :type Q: float :param R: Noise amplitude :type R: float :param delta_t: temporal discretization :type delta_t: float """ # done: add start seed self.delta_t = delta_t self.kappa_3 = kappa_3 self.Q = Q self.tau = tau self.a = self.delta_t * kappa_3 ** 2 * (tau - 1.0 / kappa_3) self.b = self.delta_t * Q / kappa_3 self.label = int(tau > 1.0 / kappa_3) self.c = np.sqrt(self.delta_t) * R self.delta_t = self.delta_t if seed is not None: np.random.seed(seed) if tau <= 1.0 / kappa_3: self.deterministic = 0.0 else: self.deterministic = kappa_3 ** 1.5 * np.sqrt((tau - 1.0 / kappa_3) / Q) def __call__(self, v): """ returns deterministic dynamic = acceleration (without noise) :param v: initial velocity vector :rtype v: ndarray :return: velocity vector of next time step :return type: ndarray """ return v * (1.0 + self.a - self.b *, v))
[docs] def simulate(self, N, v0=np.zeros(2)): """ :param N: number of time steps :type N: int :param v0: initial velocity vector :type v0: ndarray :return: time series of velocity vectors with shape (N, v0.shape[0]) :rtype: ndarray """ v = [v0] # first value is initial condition n = N - 1 # Because we are returning the initial condition, # only (N-1) time steps are computed gamma = np.random.randn(n, v0.size) for i in range(n): next_v = self.__call__(v[i]) + self.c * gamma[i] v.append(next_v) v_vec = np.array(v) return v_vec
[docs]def sample_tau(n=10, kappa_3=0.3, ratio=0.5, rel_increase=0.15): """ Return list of control parameters :param n: number of samples :type n: int :param kappa_3: inverse bifurcation point :type kappa_3: float :param ratio: ratio (default 0.5) of samples before and beyond drift-bifurcation :type ratio: float :param rel_increase: relative increase from bifurcation point :type rel_increase: float :return: tau. List of sampled bifurcation parameter :rtype tau: list """ assert ratio > 0 and ratio <= 1 assert kappa_3 > 0 assert rel_increase > 0 and rel_increase <= 1 tau_c = 1.0 / kappa_3 tau_max = tau_c * (1.0 + rel_increase) tau = tau_c + (tau_max - tau_c) * (np.random.rand(n) - ratio) return tau.tolist()
[docs]def load_driftbif(n, length, m=2, classification=True, kappa_3=0.3, seed=False): """ Simulates n time-series with length time steps each for the m-dimensional velocity of a dissipative soliton classification=True: target 0 means tau<=1/0.3, Dissipative Soliton with Brownian motion (purely noise driven) target 1 means tau> 1/0.3, Dissipative Soliton with Active Brownian motion (intrinsiv velocity with overlaid noise) classification=False: target is bifurcation parameter tau :param n: number of samples :type n: int :param length: length of the time series :type length: int :param m: number of spatial dimensions (default m=2) the dissipative soliton is propagating in :type m: int :param classification: distinguish between classification (default True) and regression target :type classification: bool :param kappa_3: inverse bifurcation parameter (default 0.3) :type kappa_3: float :param seed: random seed (default False) :type seed: float :return: X, y. Time series container and target vector :rtype X: pandas.DataFrame :rtype y: pandas.DataFrame """ # todo: add ratio of classes if m > 2: logging.warning( "You set the dimension parameter for the dissipative soliton to m={}, however it is only" "properly defined for m=1 or m=2.".format(m) ) id = np.repeat(range(n), length * m) dimensions = list(np.repeat(range(m), length)) * n labels = list() values = list() ls_tau = sample_tau(n, kappa_3=kappa_3) for i, tau in enumerate(ls_tau): ds = velocity(tau=tau, kappa_3=kappa_3, seed=seed) if classification: labels.append(ds.label) else: labels.append(ds.tau) values.append(ds.simulate(length, v0=np.zeros(m)).transpose().flatten()) time = np.stack([ds.delta_t * np.arange(length)] * n * m).flatten() df = pd.DataFrame( { "id": id, "time": time, "value": np.stack(values).flatten(), "dimension": dimensions, } ) y = pd.Series(labels) y.index = range(n) return df, y