def setUp(self):
self.datafilepath = 'test_data/data.h5'
self.netfilepath = 'test_data/network.h5'
self.netfile_new_path = 'test_data/network_new.h5'
self.test_object = SpikeCondProb(self.datafilepath, self.netfilepath, self.netfile_new_path)
class TestSpikeCondProb(unittest.TestCase):
def setUp(self):
self.datafilepath = 'test_data/data.h5'
self.netfilepath = 'test_data/network.h5'
self.netfile_new_path = 'test_data/network_new.h5'
self.test_object = SpikeCondProb(self.datafilepath, self.netfilepath, self.netfile_new_path)
def test_calc_spike_prob(self):
spike_prob = self.test_object.calc_spike_prob('TCR_0', 'SupPyrRS_1', 10e-3, 10e-3)
self.assertAlmostEqual(spike_prob, 0.5)
def test_calc_spike_prob_all_connected(self):
spike_prob = self.test_object.calc_spike_prob_all_connected(10e-3, 10e-3)
self.assertAlmostEqual(spike_prob['TCR_0-SupPyrRS_1'], 0.5)
def test_calc_spike_prob_all_unconnected(self):
spike_prob = self.test_object.calc_spike_prob_all_unconnected(10e-3, 10e-3)
self.assertAlmostEqual(spike_prob['TCR_0-SupPyrRS_0'], 0.2)
def test_calc_prespike_prob_excitatory_connected(self):
# Only 5 entries in TCR_0 are within (-15 ms, -5 ms) of spike
# time in SupPyrRS.
spike_prob = self.test_object.calc_prespike_prob_excitatory_connected(10e-3, 15e-3)
self.assertAlmostEqual(spike_prob['TCR_0-SupPyrRS_1'], 0.5)
def test_calc_prespike_prob_excitatory_unconnected(self):
spike_prob = self.test_object.calc_prespike_prob_excitatory_unconnected(5e-3, 10e-3)
self.assertAlmostEqual(spike_prob['TCR_1-SupPyrRS_1'], 0.1)
def test_calc_spike_prob_after_bgstim(self):
"""For this test data.h5 file has a /stimulus/stim_bg with
stimulus from 1.498 s to 1.5 s, second stimulus from 3.0 to
3.02 s and a third stimulus from 4.75 s to 4.77 s. Only the
spike after the first one (at 1.513 s) and the third one will be counted."""
spike_prob = self.test_object.calc_spike_prob_after_bgstim('SupPyrRS_1', 0.02, 0.01)
self.assertAlmostEqual(spike_prob, 1.0)
def test_calc_spike_prob_after_probestim(self):
spike_prob = self.test_object.calc_spike_prob_after_probestim('SupPyrRS_1', 0.02, 0.01)
self.assertAlmostEqual(spike_prob, 0.0)
def test_calc_spikecount_avg_after_bgstim(self):
"""In the spike train there is 1 spiek after 1.51 s and two
spikes after 4.78 s (4.78575 s and 4.82025 s, which is between
0.4 s amd 0.5 s after the window start."""
spike_count_avg = self.test_object.calc_spikecount_avg_after_bgstim('SupPyrRS_1', 0.05, 0.01)
self.assertAlmostEqual(spike_count_avg, 1.5)
def test_calc_spikecount_avg_after_probestim(self):
"""In the spike train there is 1 spike at 3.52325 s. The probe
stimulus ends at 3.0 s. So a delay of 0.5 s with width of 0.05
s captures this."""
spike_count_avg = self.test_object.calc_spikecount_avg_after_probestim('SupPyrRS_1', 0.05, 0.5)
self.assertAlmostEqual(spike_count_avg, 1.0)
def test_dump_stimulus_linked_probabilities(self):
filelist = ['/data/subha/rsync_ghevar_cortical_data_clone/2012_03_22/data_20120322_114922_24526.h5']
dump_stimulus_linked_probabilities(filelist, [0.01, 0.02, 0.03, 0.04, 0.05], [0.0, 0.05])
def test_get_bg_shortest_path_lengths(self):
"""The network_new.h5 file has only one TCR cell connected to a background stimulus.
This cell is connected to one of the
"""
lengths = self.test_object.get_bg_shortest_path_lengths()
self.assertEqual(len(lengths), 1)
self.assertEqual(len(lengths[lengths.keys()[0]]), 2)
def test_get_probe_shortest_path_lengths(self):
"""The network_new.h5 file has only one TCR cell (TCR_0)
connected to the probe stimulus. This cell is connected to
one of the
"""
lengths = self.test_object.get_probe_shortest_path_lengths()
self.assertEqual(len(lengths), 1)
self.assertEqual(len(lengths[lengths.keys()[0]]), 2)