def test_apical_point_smoothed():
p1 = analysis.load_file(neuron_ph_1_file)
p2 = analysis.load_file(neuron_ph_2_file)
ap1 = analysis.find_apical_point_distance_smoothed(p1, threshold=0.1)
ap2 = analysis.find_apical_point_distance_smoothed(p2, threshold=0.1)
assert_almost_equal(ap1, 355.1980697442, decimal=5)
assert_almost_equal(ap2, 199.5273018308, decimal=5)
def test_apical_point():
p1 = analysis.load_file(neuron_ph_1_file)
p2 = analysis.load_file(neuron_ph_2_file)
ap1 = analysis.find_apical_point_distance(p1)
ap2 = analysis.find_apical_point_distance(p2)
assert_almost_equal(ap1, 413.2151457659, decimal=5)
assert_almost_equal(ap2, 335.8844214625, decimal=5)
def test_load_file():
f0 = analysis.load_file(sample_ph_0_file)
f1 = analysis.load_file(sample_ph_1_file)
nt.ok_(
np.allclose(
f0,
np.array([[12.24744871, 11.18033989], [11.18033989, 10.],
[12.24744871, 0.]])))
nt.ok_(np.allclose(f1, np.array([[11.18033989, 10.], [11.18033989, 0.]])))
def test_extract_persistence_diagram():
import filecmp
if os.path.isfile('test_ph.txt'):
os.remove('test_ph.txt')
methods.extract_ph(tree0, output_file='./test_ph.txt')
ph_file = analysis.load_file('./test_ph.txt')
ph_0 = analysis.load_file(sample_ph_0)
nt.ok_(np.allclose(ph_file, ph_0))
os.remove('test_ph.txt')
def test_distance_stepped():
f0 = analysis.load_file(sample_ph_0_file)
f1 = analysis.load_file(sample_ph_1_file)
nt.ok_(analysis.distance_stepped(f0, f0) == 0.0)
nt.ok_(analysis.distance_stepped(f0, f0, order=1) == 0.0)
nt.ok_(analysis.distance_stepped(f0, f0, order=2) == 0.0)
nt.ok_(np.allclose(analysis.distance_stepped(f0, f1), 34.01795854515))
nt.ok_(
np.allclose(analysis.distance_stepped(f0, f1, order=1),
34.01795854515))
nt.ok_(
np.allclose(analysis.distance_stepped(f0, f1, order=2),
25.71017265966))