def calculate_c(m, seq, r, n):
assert r >= 0, 'Filtering threshold should be positive'
similar_vectors = 0
for i in range(0, n - m + 1):
for j in range(0, n - m + 1):
if r > ApEn.calculate_distance(seq[i], seq[j]):
similar_vectors += 1
return similar_vectors
class TestApEnCalculateDistance(unittest.TestCase, ConfigTest):
def setUp(self):
self.apEn = ApEn()
def test_calculate_distance(self):
a = [10, -4, 45.9]
b = [1, 32, -0.1]
s = self.apEn.calculate_distance(a, b)
self.assertAlmostEqual(s, 46, places=4, msg='incorrect distance')
def calc_cor_func(seq, radius):
res = []
for i in seq:
for j in seq:
res.append(
CorDim.calc_heviside(radius, ApEn.calculate_distance(i,
j)))
coef = 1 / (len(seq)**2) if len(seq) > 0 else 1
return coef * sum(res)
class TestApEnDeviation(unittest.TestCase, ConfigTest):
def setUp(self):
self.apEn = ApEn()
def test_deviation1(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
res = self.apEn.calculate_deviation(u_list)
self.assertAlmostEqual(res, 1.41185, places=4, msg='incorrect deviation')
def test_deviation2(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_4.txt'), False, 0)
res = self.apEn.calculate_deviation(u_list)
self.assertAlmostEqual(res, 2.82371, places=4, msg='incorrect deviation')
def test_deviation3(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'), False, 0)
res = self.apEn.calculate_deviation(u_list)
self.assertAlmostEqual(res, 7.05928, places=4, msg='incorrect deviation')
def test_deviation4(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_random_2-10.txt'), False, 0)
res = self.apEn.calculate_deviation(u_list)
self.assertAlmostEqual(res, 4.61831, places=4, msg='incorrect deviation')
def prepare_windows(file_name, window_size, step_size):
# 1. read the file
u_list = ApEn.read_series(file_name,
use_threshold=False,
threshold_value=0)
if not window_size:
window_size = len(u_list)
step_size = 1
assert window_size <= len(
u_list
), "Window size can't be bigger than the size of the overall sequence"
seq_list = []
for current_step in range(
floor((len(u_list) - window_size) / step_size) + 1):
next_max = current_step * step_size + window_size
if next_max > len(u_list):
break
new_seq = u_list[current_step * step_size:next_max]
seq_list.append(new_seq)
return seq_list, window_size, step_size, len(u_list)
parser = prepare_parser(launch_log_dic)
args = parser.parse_args()
check_args_combinations(parser, args)
print_processed_args(launch_log_dic, vars(args))
t = ''
use_threshold = args.entropy_use_threshold
if args.entropy_r_mode == 'STANDARD':
t = CalculationType.CONST
elif args.entropy_r_mode == 'CUSTOM':
t = CalculationType.DEV
elif args.entropy_r_mode == 'RCHON':
t = CalculationType.COMPLEX
if args.approximate_entropy:
apEn = ApEn()
report = apEn.prepare_calculate_window_apen(args.dimension, args.file_name, t, args.entropy_r_coef,
use_threshold, args.entropy_threshold_value, args.window_size,
args.window_step)
print(report)
if args.sample_entropy:
apEn = SampEn()
report = apEn.prepare_calculate_window_sampen(args.dimension, args.file_name, t, args.entropy_r_coef,
use_threshold, args.entropy_threshold_value, args.window_size,
args.window_step)
print(report)
if args.correlation_dimension:
apEn = CorDim()
report = apEn.prepare_calculate_window_cor_dim(args.file_name, args.dimension, args.correlation_dimension_radius,
args.window_size, args.window_step)
print(report)
def setUp(self):
self.apEn = ApEn()
class TestApEnPrepareCalculateApEn(unittest.TestCase, ConfigTest):
def setUp(self):
self.apEn = ApEn()
def test_prepare_calculate_const_r(self):
deviation = 1.41185
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
r = self.apEn.calculate_r(CalculationType.CONST, deviation, 0, u_list)
self.assertAlmostEqual(r, deviation * 0.2, places=4, msg='incorrect r')
def test_prepare_calculate_dev_r(self):
deviation = 1.41185
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
r = self.apEn.calculate_r(CalculationType.DEV, deviation, 0.5, u_list)
self.assertAlmostEqual(r, deviation * 0.5, places=4, msg='incorrect r')
def test_prepare_calculate_complex_r(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
deviation = self.apEn.calculate_deviation(u_list)
r = self.apEn.calculate_r(CalculationType.COMPLEX, deviation, 0.5, u_list)
self.assertAlmostEqual(r, 0.29556, places=4, msg='incorrect r')
@patch('src.core.apen.ApEn.calculate_apen')
@patch('src.core.apen.ApEn.calculate_r')
def test_prepare_calculate_r(self, mock_calculate_r, mock_calculate_apen):
mock_calculate_r.return_value = 0.28237
mock_calculate_apen.return_value=3
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
deviation = self.apEn.calculate_deviation(u_list)
r = self.apEn.calculate_r(CalculationType.COMPLEX, deviation, 0.5, u_list)
self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'),
CalculationType.CONST, 0, False, 0)
mock_calculate_r.assert_called_with(CalculationType.CONST, 1.4118572032582122, 0, u_list)
mock_calculate_apen.assert_called_with(m=2, r=r, seq=u_list)
self.assertAlmostEqual(r, 0.28237, places=4, msg='incorrect r')
class TestApEnComplexRCalculation(unittest.TestCase, ConfigTest):
def setUp(self):
self.apEn = ApEn()
def test_sdds1(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
sdds_deviation = self.apEn.make_sdds(u_list)
self.assertAlmostEqual(sdds_deviation, 1.35532, places=4, msg='incorrect sdds')
def test_sdds2(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'), False, 0)
sdds_deviation = self.apEn.make_sdds(u_list)
self.assertAlmostEqual(sdds_deviation, 6.77663, places=4, msg='incorrect sdds')
def test_complex_r_calculation1(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'), False, 0)
sdds_deviation = self.apEn.make_sdds(u_list)
deviation = self.apEn.calculate_deviation(u_list)
res = self.apEn.calculate_complex_r(sdds_deviation, deviation, len(u_list))
self.assertAlmostEqual(res, 0.29556, places=4, msg='incorrect r')
def test_complex_r_calculation2(self):
u_list = self.apEn.read_series(os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'), False, 0)
sdds_deviation = self.apEn.make_sdds(u_list)
deviation = self.apEn.calculate_deviation(u_list)
res = self.apEn.calculate_complex_r(sdds_deviation, deviation, len(u_list))
self.assertAlmostEqual(res, 0.29556, places=4, msg='incorrect r')
class TestApEnCalculateOverallApEn(unittest.TestCase, ConfigTest):
def setUp(self):
self.apEn = ApEn()
def test_calculate_apen_2_const(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'),
CalculationType.CONST, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12211, places=4, msg='incorrect ApEn')
def test_calculate_apen_2_dev(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'),
CalculationType.DEV, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12365, places=4, msg='incorrect ApEn')
def test_calculate_apen_2_complex(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_2.txt'),
CalculationType.COMPLEX, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12003, places=4, msg='incorrect ApEn')
def test_calculate_apen_4_const(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_4.txt'),
CalculationType.CONST, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12211, places=4, msg='incorrect ApEn')
def test_calculate_apen_4_dev(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_4.txt'),
CalculationType.DEV, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12365, places=4, msg='incorrect ApEn')
def test_calculate_apen_4_complex(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_4.txt'),
CalculationType.COMPLEX, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.11040, places=4, msg='incorrect ApEn')
def test_calculate_apen_10_const(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'),
CalculationType.CONST, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12211, places=4, msg='incorrect ApEn')
def test_calculate_apen_10_dev(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'),
CalculationType.DEV, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.12365, places=4, msg='incorrect ApEn')
def test_calculate_apen_10_complex(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_10.txt'),
CalculationType.COMPLEX, 0.5, False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.15675, places=4, msg='incorrect ApEn')
def test_calculate_apen_210_const(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_random_2-10.txt'),
CalculationType.CONST, 0.5,
False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.96967, places=4, msg='incorrect ApEn')
def test_calculate_apen_210_dev(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_random_2-10.txt'),
CalculationType.DEV, 0.5,
False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.67897, places=4, msg='incorrect ApEn')
def test_calculate_apen_210_complex(self):
r = self.apEn.prepare_calculate_window_apen(2, os.path.join(self.resource_path, 'ApEn_amolituda_random_2-10.txt'),
CalculationType.COMPLEX, 0.5,
False, 0)
self.assertAlmostEqual(r.get_result_value(0), 0.26964, places=4, msg='incorrect ApEn')