Source code for crikit.preprocess.tests.test_baseline_sub

"""
Testing the aysmmetric least-squares detrending algorithm

"""

import numpy as np
import numpy.testing

from crikit.preprocess.subtract_baseline import SubtractBaselineALS

[docs]def test_basic(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) als = SubtractBaselineALS(smoothness_param=1, asym_param=1e-3, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert y_als.max() < 0.0004
[docs]def test_fix_ends(): x = np.linspace(-100, 100, 1000) y = 1000*np.exp(-x**2/(2*20**2)) + 200*np.exp(-(x+99)**2/(2*1**2)) als = SubtractBaselineALS(smoothness_param=1e2, asym_param=1e-3, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert y_als[0] > 20 als = SubtractBaselineALS(smoothness_param=1e1, asym_param=1e-3, redux=1, fix_end_points=True, fix_rng=None, verbose=True) y_als = als.calculate(y) assert y_als[0] < 2
[docs]def test_fix_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) fix_rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1e3, asym_param=1e-5, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[200:800]) > 0.002 als = SubtractBaselineALS(smoothness_param=1e3, asym_param=1e-5, redux=1, fix_end_points=False, fix_rng=fix_rng, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[200:800]) < 0.002
[docs]def test_vec_asym_param(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) asym_param = 1e-6*np.ones((x.size)) als = SubtractBaselineALS(smoothness_param=1e3, asym_param=asym_param, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[250:750]) > 7 asym_param[200:800] = 1e-2 als = SubtractBaselineALS(smoothness_param=1e3, asym_param=asym_param, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[250:750]) < 0.03
[docs]def test_basic_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1, asym_param=1e-3, rng=rng, redux=1, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) np.testing.assert_almost_equal(y_als[...,rng], 0, decimal=2) np.testing.assert_allclose(y_als[:200],0) np.testing.assert_allclose(y_als[800:],0)
[docs]def test_basic_redux(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) als = SubtractBaselineALS(smoothness_param=1e-2, asym_param=1e-1, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) np.testing.assert_almost_equal(y_als, 0, decimal=3)
[docs]def test_basic_redux_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1e-2, asym_param=1e-1, rng=rng, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) np.testing.assert_allclose(y_als[:200],0) np.testing.assert_allclose(y_als[800:],0) np.testing.assert_almost_equal(y_als[...,rng], 0, decimal=3)
[docs]def test_2Dbasic_redux_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) y = np.dot(np.ones((10,1)), y[None,:]) rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1e-2, asym_param=1e-1, rng=rng, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) np.testing.assert_allclose(y_als[..., :200],0) np.testing.assert_allclose(y_als[..., 800:],0) np.testing.assert_almost_equal(y_als[...,rng], 0, decimal=3)
[docs]def test_2Dbasic_transform_redux_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) y = np.dot(np.ones((10,1)), y[None,:]) rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1e-2, asym_param=1e-1, rng=rng, redux=10, fix_end_points=False, fix_rng=None, verbose=True) als.transform(y) np.testing.assert_allclose(y[..., :200],0) np.testing.assert_allclose(y[..., 800:],0) np.testing.assert_almost_equal(y[...,rng], 0, decimal=3)
[docs]def test_vec_asym_param_rng_redux(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) asym_param = 1e-7*np.ones((x.size)) als = SubtractBaselineALS(smoothness_param=1, asym_param=asym_param, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[250:750]) > 7 asym_param[200:800] = 1e-1 als = SubtractBaselineALS(smoothness_param=1, asym_param=asym_param, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max((y_als)[250:750]) < 0.03
[docs]def test_rng_redux_fix_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) als = SubtractBaselineALS(smoothness_param=1, asym_param=1e-7, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max(y_als[250:750]) > 9 fix_rng = np.arange(200,800) als = SubtractBaselineALS(smoothness_param=1, asym_param=1e-7, redux=10, fix_end_points=False, fix_rng=fix_rng, verbose=True) y_als = als.calculate(y) assert np.max(y_als[250:750]) < 0.004