def test_bad_start(self):
folder = os.path.dirname(os.path.realpath(__file__))
time = np.load(os.path.join(folder, "data/t_spike.npy"))
values = np.load(os.path.join(folder, "data/V_spike.npy"))
spikes = Spikes()
spikes.find_spikes(time, values)
self.assertEqual(len(spikes), 14)
def test_noisy(self):
folder = os.path.dirname(os.path.realpath(__file__))
time = np.load(os.path.join(folder, "data/t_noise.npy"))
values = np.load(os.path.join(folder, "data/V_noise.npy"))
spikes = Spikes()
spikes.find_spikes(time, values)
spikes.plot_voltage("voltage.png")
self.assertEqual(len(spikes), 16)
class TestSpikes(TestCasePlot):
def setUp(self):
folder = os.path.dirname(os.path.realpath(__file__))
self.time = np.load(os.path.join(folder, "data/t_test.npy"))
self.values = np.load(os.path.join(folder, "data/U_test.npy"))
self.output_test_dir = ".tests/"
if os.path.isdir(self.output_test_dir):
shutil.rmtree(self.output_test_dir)
os.makedirs(self.output_test_dir)
self.figureformat = ".png"
def tearDown(self):
if os.path.isdir(self.output_test_dir):
shutil.rmtree(self.output_test_dir)
def test_init_no_input(self):
self.spikes = Spikes()
self.assertIsInstance(self.spikes, Spikes)
def test_init_input(self):
self.spikes = Spikes(self.time, self.values)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_default(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_auto(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, threshold="auto")
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_extended(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, extended_spikes=True)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_default_auto_extended(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time,
self.values,
threshold="auto",
extended_spikes=True)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_iter(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
for spike in self.spikes:
self.assertIsInstance(spike, Spike)
def test_len(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
self.assertEqual(len(self.spikes), 12)
def test_getitem(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
result = self.spikes[0]
self.assertIsInstance(result, Spike)
def test_plot(self):
self.spikes = Spikes(self.time,
self.values,
xlabel="xlabel",
ylabel="ylabel")
self.spikes.plot(os.path.join(self.output_test_dir, "spikes.png"))
self.plot_exists("spikes")
def test_plot_extended(self):
self.spikes = Spikes(self.time,
self.values,
xlabel="xlabel",
ylabel="ylabel",
extended_spikes=True)
self.spikes.plot(
os.path.join(self.output_test_dir, "spikes_extended.png"))
self.plot_exists("spikes_extended")
def plot_exists(self, name):
plot_file = os.path.join(self.output_test_dir, name + ".png")
self.assertTrue(os.path.isfile(plot_file))
class TestSpikes(TestCasePlot):
def setUp(self):
folder = os.path.dirname(os.path.realpath(__file__))
self.time = np.load(os.path.join(folder, "data/t_test.npy"))
self.values = np.load(os.path.join(folder, "data/U_test.npy"))
self.output_test_dir = ".tests/"
if os.path.isdir(self.output_test_dir):
shutil.rmtree(self.output_test_dir)
os.makedirs(self.output_test_dir)
self.figureformat = ".png"
def tearDown(self):
if os.path.isdir(self.output_test_dir):
shutil.rmtree(self.output_test_dir)
def test_init_no_input(self):
self.spikes = Spikes()
self.assertIsInstance(self.spikes, Spikes)
def test_init_input(self):
self.spikes = Spikes(self.time, self.values)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_default(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_auto(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, threshold="auto")
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_min_amplitude(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, min_amplitude=1000)
self.assertEqual(self.spikes.nr_spikes, 0)
def test_find_spikes_min_duration(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, min_duration=1000)
self.assertEqual(self.spikes.nr_spikes, 0)
def test_str(self):
self.spikes = Spikes(self.time, self.values)
self.assertIsInstance(str(self.spikes), str)
def test_find_spikes_extended(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, extended_spikes=True)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_default_auto_extended(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, threshold="auto", extended_spikes=True)
self.assertEqual(self.spikes.nr_spikes, 12)
def test_find_spikes_normalize(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values, threshold=0.4, end_threshold=-0.1, normalize=True)
self.assertEqual(self.spikes.nr_spikes, 12)
self.assertTrue(self.spikes[0].V_spike > 1)
def test_find_spikes_normalize_error(self):
self.spikes = Spikes()
with self.assertRaises(ValueError):
self.spikes.find_spikes(self.time, self.values, threshold=12, end_threshold=-0.1, normalize=True)
with self.assertRaises(ValueError):
self.spikes.find_spikes(self.time, self.values, threshold=0.1, end_threshold=12, normalize=True)
def test_iter(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
for spike in self.spikes:
self.assertIsInstance(spike, Spike)
def test_len(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
self.assertEqual(len(self.spikes), 12)
def test_getitem(self):
self.spikes = Spikes()
self.spikes.find_spikes(self.time, self.values)
result = self.spikes[0]
self.assertIsInstance(result, Spike)
def test_plot_spikes(self):
self.spikes = Spikes(self.time, self.values, xlabel="xlabel", ylabel="ylabel")
self.spikes.plot_spikes(os.path.join(self.output_test_dir, "spikes.png"))
self.plot_exists("spikes")
def test_plot_voltage(self):
self.spikes = Spikes(self.time, self.values, xlabel="xlabel", ylabel="ylabel")
self.spikes.plot_spikes(os.path.join(self.output_test_dir, "voltage.png"))
self.plot_exists("voltage")
def test_plot_extended(self):
self.spikes = Spikes(self.time, self.values, xlabel="xlabel", ylabel="ylabel", extended_spikes=True)
self.spikes.plot_spikes(os.path.join(self.output_test_dir, "spikes_extended.png"))
self.plot_exists("spikes_extended")
def plot_exists(self, name):
plot_file = os.path.join(self.output_test_dir, name + ".png")
self.assertTrue(os.path.isfile(plot_file))
def test_bad_start(self):
folder = os.path.dirname(os.path.realpath(__file__))
time = np.load(os.path.join(folder, "data/t_spike.npy"))
values = np.load(os.path.join(folder, "data/V_spike.npy"))
spikes = Spikes()
spikes.find_spikes(time, values)
self.assertEqual(len(spikes), 14)
def test_noisy(self):
folder = os.path.dirname(os.path.realpath(__file__))
time = np.load(os.path.join(folder, "data/t_noise.npy"))
values = np.load(os.path.join(folder, "data/V_noise.npy"))
spikes = Spikes()
spikes.find_spikes(time, values)
spikes.plot_voltage("voltage.png")
self.assertEqual(len(spikes), 16)