def test_simple_calculate_columns(self):
query = np.arange(13)
series = np.arange(23)
m = 4
distance_matrix1 = np.arange(200.).reshape((10, 20))
distance_matrix2 = np.ones((10, 20), dtype=np.float)
distance_matrix3 = np.full((10, 20), np.nan, dtype=np.float)
distance_matrix4 = np.full((10, 20), 5., dtype=np.float)
calc = AnytimeCalculator(m, series, query)
calc.add_generator(0, MockGenerator(distance_matrix1))
calc.add_generator(0, MockGenerator(distance_matrix2))
calc.add_generator(0, MockGenerator(distance_matrix3))
calc.add_generator(0, MockGenerator(distance_matrix4))
consumer1 = DistanceMatrix()
consumer2 = DistanceMatrix()
consumer3 = SummingConsumer()
calc.add_consumer([0], consumer1)
calc.add_consumer([3], consumer2)
calc.add_consumer([0, 1, 3], consumer3)
calc.calculate_columns()
npt.assert_equal(consumer1.distance_matrix, distance_matrix1)
npt.assert_equal(consumer2.distance_matrix, distance_matrix4)
npt.assert_equal(
consumer3.distance_matrix,
distance_matrix1 + distance_matrix2 + distance_matrix4)
def test_simple_calculate_diagonals_partial(self):
query = np.arange(13)
series = np.arange(23)
m = 4
distance_matrix1 = np.arange(200.).reshape((10, 20))
distance_matrix2 = np.ones((10, 20), dtype=np.float)
distance_matrix3 = np.full((10, 20), np.nan, dtype=np.float)
distance_matrix4 = np.full((10, 20), 5., dtype=np.float)
summed_matrix = distance_matrix1 + distance_matrix2 + distance_matrix4
max_diag = min(len(query) - m + 1,
len(series) - m + 1) # Maximum length of a diagonal
calc = AnytimeCalculator(m, series, query)
calc.add_generator(0, MockGenerator(distance_matrix1))
calc.add_generator(0, MockGenerator(distance_matrix2))
calc.add_generator(0, MockGenerator(distance_matrix3))
calc.add_generator(0, MockGenerator(distance_matrix4))
consumer1 = DistanceMatrix()
consumer2 = DistanceMatrix()
consumer3 = SummingConsumer()
calc.add_consumer([0], consumer1)
calc.add_consumer([3], consumer2)
calc.add_consumer([0, 1, 3], consumer3)
calc.calculate_diagonals(partial=20)
npt.assert_(20 <= np.count_nonzero(
~np.isnan(consumer1.distance_matrix) < 20 + max_diag))
npt.assert_(20 <= np.count_nonzero(
~np.isnan(consumer2.distance_matrix) < 20 + max_diag))
npt.assert_(20 <= np.count_nonzero(
~np.isnan(consumer3.distance_matrix) < 20 + max_diag))
# For 20 items, at least 3 diagonals are calculated
for diagonal in calc._diagonal_calc_order[:3]:
diag_indices = diag_indices_of(distance_matrix1, diagonal)
npt.assert_equal(consumer1.distance_matrix[diag_indices],
distance_matrix1[diag_indices])
calc.calculate_diagonals(partial=.8)
npt.assert_(160 <= np.count_nonzero(
~np.isnan(consumer1.distance_matrix) < 160 + max_diag))
npt.assert_(160 <= np.count_nonzero(
~np.isnan(consumer2.distance_matrix) < 160 + max_diag))
npt.assert_(160 <= np.count_nonzero(
~np.isnan(consumer3.distance_matrix) < 160 + max_diag))
calc.calculate_diagonals()
npt.assert_(
200 == np.count_nonzero(~np.isnan(consumer1.distance_matrix)))
npt.assert_(
200 == np.count_nonzero(~np.isnan(consumer2.distance_matrix)))
npt.assert_(
200 == np.count_nonzero(~np.isnan(consumer3.distance_matrix)))
npt.assert_equal(consumer1.distance_matrix, distance_matrix1)
npt.assert_equal(consumer2.distance_matrix, distance_matrix4)
npt.assert_equal(consumer3.distance_matrix, summed_matrix)
def test_simple_calculate_columns_partial(self):
query = np.arange(13)
series = np.arange(23)
m = 4
distance_matrix1 = np.arange(200.).reshape((10, 20))
distance_matrix2 = np.ones((10, 20), dtype=np.float)
distance_matrix3 = np.full((10, 20), np.nan, dtype=np.float)
distance_matrix4 = np.full((10, 20), 5., dtype=np.float)
summed_matrix = distance_matrix1 + distance_matrix2 + distance_matrix4
calc = AnytimeCalculator(m, series, query)
calc.add_generator(0, MockGenerator(distance_matrix1))
calc.add_generator(0, MockGenerator(distance_matrix2))
calc.add_generator(0, MockGenerator(distance_matrix3))
calc.add_generator(0, MockGenerator(distance_matrix4))
consumer1 = DistanceMatrix()
consumer2 = DistanceMatrix()
consumer3 = SummingConsumer()
calc.add_consumer([0], consumer1)
calc.add_consumer([3], consumer2)
calc.add_consumer([0, 1, 3], consumer3)
# Calculates [3..12[
calc.calculate_columns(start=3, upto=0.6)
npt.assert_equal(consumer1.distance_matrix,
copy_columns(distance_matrix1, range(3, 12)))
npt.assert_equal(consumer2.distance_matrix,
copy_columns(distance_matrix4, range(3, 12)))
npt.assert_equal(consumer3.distance_matrix,
copy_columns(summed_matrix, range(3, 12)))
# Calculates [12..15[
calc.calculate_columns(upto=15)
npt.assert_equal(consumer1.distance_matrix,
copy_columns(distance_matrix1, range(3, 15)))
npt.assert_equal(consumer2.distance_matrix,
copy_columns(distance_matrix4, range(3, 15)))
npt.assert_equal(consumer3.distance_matrix,
copy_columns(summed_matrix, range(3, 15)))
# Calculates [15..20[
calc.calculate_columns()
npt.assert_equal(consumer1.distance_matrix,
copy_columns(distance_matrix1, range(3, 20)))
npt.assert_equal(consumer2.distance_matrix,
copy_columns(distance_matrix4, range(3, 20)))
npt.assert_equal(consumer3.distance_matrix,
copy_columns(summed_matrix, range(3, 20)))
# Calculates [0..3[
calc.calculate_columns(start=0., upto=3)
npt.assert_equal(consumer1.distance_matrix, distance_matrix1)
npt.assert_equal(consumer2.distance_matrix, distance_matrix4)
npt.assert_equal(consumer3.distance_matrix, summed_matrix)
def test_simple_calculate_self_join_columns(self):
series = np.arange(23)
m = 4
buffer = 2
distance_matrix = np.arange(1., 401.).reshape((20, 20))
calc = AnytimeCalculator(m, series, trivial_match_buffer=buffer)
calc.add_generator(0, MockGenerator(distance_matrix))
consumer = DistanceMatrix()
calc.add_consumer([0], consumer)
calc.calculate_columns()
expected = distance_matrix.copy()
for diag in range(-buffer, buffer + 1):
expected[diag_indices_of(expected, diag)] = np.inf
npt.assert_equal(consumer.distance_matrix, expected)
def test_simple_calculate_self_join_diagonals(self):
series = np.arange(23)
m = 4
buffer = 2
# This test verifies that no values below the main diagonal are used.
distance_matrix = np.triu(
np.arange(1., 401.).reshape((20, 20)), buffer + 1)
calc = AnytimeCalculator(m, series, trivial_match_buffer=buffer)
calc.add_generator(0, MockGenerator(distance_matrix))
consumer = DistanceMatrix()
calc.add_consumer([0], consumer)
npt.assert_array_less(np.full(17, buffer), calc._diagonal_calc_order)
calc.calculate_diagonals()
expected = distance_matrix + distance_matrix.T
expected[expected == 0] = np.nan
npt.assert_equal(consumer.distance_matrix, expected)
def find_consensus_motif_bruteforce(series_list, m) -> CMResult:
result = CMResult(np.inf, -1, -1)
for series_idx, series in enumerate(series_list):
radii = np.zeros(len(series) - m + 1)
for series2_idx, series2 in enumerate(series_list):
if series_idx == series2_idx:
continue
calc = AnytimeCalculator(m, series, series2)
calc.add_generator(0, ZNormEuclidean())
mp_cons = calc.add_consumer([0], MatrixProfileLR())
calc.calculate_columns()
mp = mp_cons.matrix_profile()
radii = np.maximum(radii, mp)
subseq_idx = np.argmin(radii)
subseq_radius = radii[subseq_idx]
if subseq_radius < result.radius:
result = CMResult(subseq_radius, series_idx, subseq_idx)
return result
from distancematrix.calculator import AnytimeCalculator
from distancematrix.generator.znorm_euclidean import ZNormEuclidean
from distancematrix.consumer.matrix_profile_lr import MatrixProfileLR
import numpy as np
from src.series import Series
m = 10
# Create some random data
np.random.seed(123)
data = np.array(np.random.rand(100))
# Calculate the matrix profile
calculator = AnytimeCalculator(m, [data])
generator = calculator.add_generator(
0, ZNormEuclidean(noise_std=0.)) # Generator 0 works on channel 0
consumer = calculator.add_consumer([0], MatrixProfileLR())
calculator.calculate_diagonals()
# The matrix profile
left_matrix_profile = consumer.matrix_profile_left
profile_index_left = consumer.profile_index_left
class TestSeries(TestCase):
def test_it_should_open_the_result_file_as_appending(self):
mock = mock_open()
with patch('builtins.open', mock):
series = Series('key', [m], 1000, './test')