def setUp(self):
"""Creates test data"""
random_state = np.random.RandomState(0)
modes_location = np.concatenate(
(random_state.normal(-.3, .04, size=15),
random_state.normal(.3, .04, size=15)))
idx = np.arange(30)
random_state.shuffle(idx)
modes_location = modes_location[idx]
self.modes_location = modes_location
self.y = np.array(15 * [0] + 15 * [1])[idx]
self.X = make_multimodal_samples(n_samples=30,
modes_location=modes_location,
noise=.05,
random_state=random_state)
self.X2 = make_multimodal_samples(n_samples=30,
modes_location=modes_location,
noise=.05,
random_state=1)
self.probs = np.array(15 * [[1., 0.]] + 15 * [[0., 1.]])[idx]
# Dataset with outliers
fd_clean = make_sinusoidal_process(n_samples=25, error_std=0,
phase_std=0.1, random_state=0)
fd_outliers = make_sinusoidal_process(n_samples=2, error_std=0,
phase_mean=0.5, random_state=5)
self.fd_lof = fd_outliers.concatenate(fd_clean)
def test_shift_registration(self):
"""Test wrapper of shift_registration_deltas"""
fd = make_sinusoidal_process(n_samples=2, error_std=0, random_state=1)
fd_reg = shift_registration(fd)
deltas = shift_registration_deltas(fd)
np.testing.assert_array_almost_equal(fd_reg.data_matrix,
fd.shift(deltas).data_matrix)
def test_shift_registration_deltas(self):
fd = make_sinusoidal_process(n_samples=2, error_std=0, random_state=1)
deltas = shift_registration_deltas(fd).round(3)
np.testing.assert_array_almost_equal(deltas, [-0.022, 0.03])
fd = fd.to_basis(Fourier())
deltas = shift_registration_deltas(fd).round(3)
np.testing.assert_array_almost_equal(deltas, [-0.022, 0.03])
def test_fit_and_transform(self):
"""Test wrapper of shift_registration_deltas"""
fd = make_sinusoidal_process(n_samples=2, error_std=0, random_state=10)
reg = ShiftRegistration()
response = reg.fit(self.fd)
# Check attributes and returned value
self.assertTrue(hasattr(reg, 'template_'))
self.assertTrue(response is reg)
fd_registered = reg.transform(fd)
deltas = reg.deltas_.round(3)
np.testing.assert_allclose(deltas, [0.071, -0.072])
import matplotlib.pyplot as plt from skfda.datasets import make_sinusoidal_process from skfda.preprocessing.registration import ShiftRegistration from skfda.representation.basis import Fourier ############################################################################## # In this example we will use a # :func:`sinusoidal process <skfda.datasets.make_sinusoidal_process>` # synthetically generated. This dataset consists in a sinusoidal wave with # fixed period which contanis phase and amplitude variation with gaussian # noise. # # In this example we want to register the curves using a translation # and remove the phase variation to perform further analysis. fd = make_sinusoidal_process(random_state=1) fd.plot() ############################################################################## # We will smooth the curves using a basis representation, which will help us # to remove the gaussian noise. Smoothing before registration # is essential due to the use of derivatives in the optimization process. # Because of their sinusoidal nature we will use a Fourier basis. fd_basis = fd.to_basis(Fourier(n_basis=11)) fd_basis.plot() ############################################################################## # We will use the # :func:`~skfda.preprocessing.registration.ShiftRegistration` transformer, # which is suitable due to the periodicity of the dataset and the small
import skfda
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d
from skfda.datasets import make_sinusoidal_process
from skfda.representation.interpolation import SplineInterpolator
fd = make_sinusoidal_process(n_samples=1, n_features=6, random_state=3) + 1.2
fd.interpolator = SplineInterpolator(interpolation_order=3)
plt.figure("original-function")
fd.scatter(label='original values')
fd.plot(label='interpolation', color='C0', linestyle="--")
plt.legend()
x = fd.sample_points[0]
y = fd.data_matrix.squeeze()
ymin, ymax = plt.ylim()
ymin = 0
for i in range(len(x)):
plt.plot([x[i], x[i]], [-1.2, y[i]], color='C0', linewidth=1)
plt.ylim(ymin, ymax)
plt.yticks([])
plt.tight_layout()
plt.figure("function-resampled")
def setUp(self):
"""Initialization of samples"""
self.X = make_sinusoidal_process(error_std=0, random_state=0)
self.shift_registration = ShiftRegistration().fit(self.X)
def setUp(self):
"""Initialization of samples"""
self.fd = make_sinusoidal_process(n_samples=2,
error_std=0,
random_state=1)
self.fd.extrapolation = "periodic"
def setUp(self):
self.grid = make_sinusoidal_process(n_samples=2, random_state=0)
self.basis = self.grid.to_basis(Fourier())
self.dummy_data = [[1, 2, 3], [2, 3, 4]]
# a FDataGrid representing a function :math:`f : \mathbb{R}^2\longmapsto\mathbb{R}^2` is
# constructed to show also the support of a multivariate dimensional image. The first
# dimension of the image contains sinusoidal processes and the second dimension,
# gaussian ones.
#
# First, the values are generated for each dimension with a function
# :math:`f : \mathbb{R}\longmapsto\mathbb{R}` implemented in the
# :func:`make_sinusoidal_process method <skfda.datasets.make_sinusoidal_process>` and in the
# :func:`make_gaussian_process method <skfda.datasets.make_gaussian_process>`, respectively.
# Those functions return FDataGrid objects whose 'data_matrix' store the values needed.
n_samples = 10
n_features = 10
fd1 = make_sinusoidal_process(n_samples=n_samples,
n_features=n_features,
random_state=5)
fd1.dataset_label = "Sinusoidal process"
fd2 = make_gaussian_process(n_samples=n_samples,
n_features=n_features,
random_state=1)
fd2.dataset_label = "Brownian process"
##################################################################################
# After, those values generated for one dimension on the domain are propagated along
# another dimension, obtaining a three-dimensional matrix or cube (two-dimensional domain
# and one-dimensional image). This is done with both data matrices from the above FDataGrids.
cube1 = np.repeat(fd1.data_matrix, n_features).reshape(
(n_samples, n_features, n_features))
cube2 = np.repeat(fd2.data_matrix, n_features).reshape(
