k-shape/test.py

import math
import numpy as np

from numpy.random import randint
from numpy.linalg import norm
from numpy.fft import fft, ifft

from scipy.sparse.linalg import eigs
from scipy.stats import zscore
from scipy.ndimage.interpolation import shift

def ncc_c(x,y):
    """
    >>> ncc_c([1,2,3,4], [1,2,3,4])
    array([ 0.13333333,  0.36666667,  0.66666667,  1.        ,  0.66666667,
            0.36666667,  0.13333333])
    >>> ncc_c([1,1,1], [1,1,1])
    array([ 0.33333333,  0.66666667,  1.        ,  0.66666667,  0.33333333])
    >>> ncc_c([1,2,3], [-1,-1,-1])
    array([-0.15430335, -0.46291005, -0.9258201 , -0.77151675, -0.46291005])
    """
    x_len = len(x)
    fft_size = 1<<(2*x_len-1).bit_length()
    cc = ifft(fft(x, fft_size) * np.conj(fft(y, fft_size)))
    cc = np.concatenate((cc[-(x_len-1):], cc[:x_len]))
    return np.real(cc) / (norm(x) * norm(y))


def sbd(x, y):
    """
    >>> sbd([1,1,1], [1,1,1])
    (-2.2204460492503131e-16, array([1, 1, 1]))
    >>> sbd([0,1,2], [1,2,3])
    (0.043817112532485103, array([1, 2, 3]))
    >>> sbd([1,2,3], [0,1,2])
    (0.043817112532485103, array([0, 1, 2]))
    """
    ncc = ncc_c(x, y)
    idx = ncc.argmax()
    dist = 1 - ncc[idx]
    yshift = shift(y, (idx + 1) - max(len(x), len(y)))
    return dist, yshift

def extract_shape(idx, x, j, cur_center):
    """
    >>> extract_shape(np.array([0,1,2]), np.array([[1,2,3], [4,5,6]]), 1, np.array([0,3,4]))
    array([ -1.00000000e+00,  -3.06658683e-19,   1.00000000e+00])
    >>> extract_shape(np.array([0,1,2]), np.array([[-1,2,3], [4,-5,6]]), 1, np.array([0,3,4]))
    array([-0.96836405,  1.02888681, -0.06052275])
    """
    _a = []
    for i in range(len(idx)):
        if idx[i] == j:
            if cur_center.sum() == 0:
                opt_x = x[i]
            else:
                _, opt_x = sbd(cur_center, x[i])
            _a.append(opt_x)
    a = np.array(_a)

    if len(a) == 0:
        return np.zeros((1, x.shape[1]))
    columns = a.shape[1]
    y = zscore(a,axis=1,ddof=1)
    s = np.dot(y.transpose(), y)

    p = np.empty((columns, columns))
    p.fill(1.0/columns)
    p = np.eye(columns) - p

    m = np.dot(np.dot(p, s), p)
    _, vec = eigs(m, 1)
    centroid = np.real(vec[:,0])
    finddistance1 = math.sqrt(((a[0] - centroid) ** 2).sum())
    finddistance2 = math.sqrt(((a[0] + centroid) ** 2).sum())

    if finddistance1 >= finddistance2:
        centroid *= -1
    return zscore(centroid, ddof=1)


def kshape(x, k):
    """
    >>> kshape(np.array([[1,2,3,4], [0,1,2,3], [-1,1,-1,1], [1,2,2,3]]), 2)
    (array([0, 0, 1, 0]), array([[-1.19623139, -0.26273649,  0.26273649,  1.19623139],
           [-0.8660254 ,  0.8660254 , -0.8660254 ,  0.8660254 ]]))
    """
    m = x.shape[0]
    idx = randint(0, k, size=m)
    centroids = np.zeros((k,x.shape[1]))

    distances = np.empty((m, k))
    for _ in range(100):
        old_idx = idx
        for j in range(k):
            res = extract_shape(idx, x, j, centroids[j])
            centroids[j] = res

        for i in range(m):
            for j in range(k):
                distances[i,j] = 1 - max(ncc_c(x[i], centroids[j]))
        idx = distances.argmin(1)
        if norm(old_idx - idx) == 0:
            break
    return idx, centroids


if __name__ == "__main__":
    import doctest
    doctest.testmod()