def test_dtw_subseq_bug1():
use_c = True
with util_numpy.test_uses_numpy() as np:
query = np.array([-0.86271501, -1.32160597, -1.2307838, -0.97743775, -0.88183547,
-0.71453147, -0.70975136, -0.65238999, -0.48508599, -0.40860416,
-0.5567877, -0.39904393, -0.51854679, -0.51854679, -0.23652005,
-0.21261948, 0.16978966, 0.21281068, 0.6573613, 1.28355626,
1.88585065, 1.565583, 1.40305912, 1.64206483, 1.8667302])
s1 = np.array([-0.87446789, 0.50009064, -1.43396157, 0.52081263, 1.28752619])
s2 = np.array([1.19125347, 0.78778189, -0.95770272, -1.02133264])
sa = subsequence_alignment(query, s1, use_c=use_c)
assert sa.best_match().value == pytest.approx(0.08735692337954708)
sa = subsequence_alignment(query, s2, use_c=use_c)
assert sa.best_match().value == pytest.approx(0.25535859535443606)
def test_dtw_subseq1():
with util_numpy.test_uses_numpy() as np:
query = np.array([1., 2, 0])
series = np.array([1., 0, 1, 2, 1, 0, 2, 0, 3, 0, 0])
sa = subsequence_alignment(query, series)
mf = sa.matching_function()
# print(f'{mf=}')
match = sa.best_match()
# print(match)
# print(f'Segment={match.segment}')
# print(f'Path={match.path}')
if not dtwvis.test_without_visualization():
try:
import matplotlib.pyplot as plt
except ImportError:
raise MatplotlibException("No matplotlib available")
if directory:
plt.plot(mf)
plt.savefig(directory / "subseq_matching.png")
dtwvis.plot_warpingpaths(query,
series,
sa.warping_paths(),
match.path,
filename=directory /
"subseq_warping.png")
plt.close()
best_k = sa.kbest_matches(k=3)
assert match.path == [(0, 2), (1, 3), (2, 4)]
assert [m.segment for m in best_k] == [[2, 4], [5, 7], [0, 1]]
def test_dtw_subseq_ndim():
use_c = False
with util_numpy.test_uses_numpy() as np:
# s1 = np.array([1., 2, 3,1])
# query = np.array([2.0, 3.1])
s1 = np.array([[1., 1], [2, 2], [3, 3], [1, 1]])
query = np.array([[2.0, 2.1], [3.1, 3.0]])
sa = subsequence_alignment(query, s1, use_c=use_c)
m = sa.best_match()
assert m.segment == [1, 2]
assert m.value == pytest.approx(0.07071067811865482)
def test_dtw_subseq_eeg():
with util_numpy.test_uses_numpy() as np:
data_fn = Path(__file__).parent / 'rsrc' / 'EEGRat_10_1000.txt'
data = np.loadtxt(data_fn)
series = np.array(data[1500:1700])
query = np.array(data[1331:1352])
sa = subsequence_alignment(query, series)
match = sa.best_match()
kmatches = list(sa.kbest_matches(k=15, overlap=0))
segments = [m.segment for m in kmatches]
segments_sol = [[38, 56], [19, 37], [167, 185], [124, 143], [84, 100],
[59, 77], [150, 162], [101, 121], [0, 15]]
assert segments == segments_sol
if directory and not dtwvis.test_without_visualization():
try:
import matplotlib.pyplot as plt
except ImportError:
raise MatplotlibException("No matplotlib available")
fn = directory / "test_dtw_subseq_eeg1.png"
fig = plt.figure(figsize=(20, 30))
dtwvis.plot_warpingpaths(query,
series,
sa.warping_paths(),
match.path,
figure=fig)
plt.savefig(fn)
plt.close(fig)
fn = directory / "test_dtw_subseq_eeg2.png"
startidx, endidx = match.segment
fig = plt.figure()
plt.plot(query, label='query')
plt.plot(series[startidx:endidx], label='best match')
plt.legend()
plt.savefig(fn)
plt.close(fig)
fn = directory / "test_dtw_subseq_eeg3.png"
fig = plt.figure(figsize=(20, 10))
fig, ax = dtwvis.plot_warpingpaths(query,
series,
sa.warping_paths(),
path=-1,
figure=fig)
print(f'plotting {len(kmatches)} matches')
for kmatch in kmatches:
dtwvis.plot_warpingpaths_addpath(ax, kmatch.path)
plt.savefig(fn)
plt.close(fig)