def test_path_ctor():
# make sure constructors that take file paths can use pathlib.Path
path = pathlib.Path(PATH)
NodeStorage(path / 'nodes1.h5')
EdgeStorage(path / 'edges1.h5')
SpikeReader(path / 'spikes.h5')
SomaReportReader(path / 'somas.h5')
ElementReportReader(path / 'elements.h5')
def test_path_ctor():
# make sure constructors that take file paths can use pathlib.Path
path = pathlib.Path(PATH)
NodeStorage(path / 'nodes1.h5')
EdgeStorage(path / 'edges1.h5')
SpikeReader(path / 'spikes.h5')
SomaReportReader(path / 'somas.h5')
ElementReportReader(path / 'elements.h5')
NodeSets.from_file(path / 'node_sets.json')
CircuitConfig.from_file(path / 'config/circuit_config.json')
class TestElementReportPopulation(unittest.TestCase):
def setUp(self):
path = os.path.join(PATH, "elements.h5")
self.test_obj = ElementReportReader(path)
def test_get_all_population(self):
self.assertEqual(self.test_obj.get_populations_names(),
['All', 'element1', 'element42'])
def test_get_population(self):
self.assertTrue(
isinstance(self.test_obj['All'], ElementReportPopulation))
def test_get_inexistant_population(self):
self.assertRaises(RuntimeError, self.test_obj.__getitem__, 'foobar')
def test_get_reports_from_population(self):
self.assertEqual(self.test_obj['All'].times, (0., 4., 0.2))
self.assertEqual(self.test_obj['All'].time_units, 'ms')
self.assertEqual(self.test_obj['All'].data_units, 'mV')
self.assertTrue(self.test_obj['All'].sorted)
self.assertEqual(len(self.test_obj['All'].get().data),
100) # Number of elements
sel = self.test_obj['All'].get(node_ids=[13, 14],
tstart=0.8,
tstop=1.2)
keys = list(sel.data.keys())
keys.sort()
self.assertEqual(keys,
[(13, 60), (13, 61), (13, 62), (13, 63), (13, 64),
(14, 65), (14, 66), (14, 67), (14, 68), (14, 69)])
self.assertEqual(len(sel.index),
3) # Number of timestamp (0.8, 1.0 and 1.2)
sel = self.test_obj['All'].get(tstart=5.,
tstop=-1) # tstart out of range
self.assertEqual(len(sel.data), 0)
sel = self.test_obj['All'].get(tstart=3., tstop=3.)
self.assertEqual(len(sel.data), 100)
def setUp(self):
path = os.path.join(PATH, "elements.h5")
self.test_obj = ElementReportReader(path)
class TestElementReportPopulation(unittest.TestCase):
def setUp(self):
path = os.path.join(PATH, "elements.h5")
self.test_obj = ElementReportReader(path)
def test_get_all_population(self):
self.assertEqual(self.test_obj.get_population_names(),
['All', 'element1', 'element42'])
def test_get_population(self):
self.assertTrue(
isinstance(self.test_obj['All'], ElementReportPopulation))
def test_get_inexistant_population(self):
self.assertRaises(RuntimeError, self.test_obj.__getitem__, 'foobar')
def test_get_node_ids(self):
self.assertEqual(self.test_obj['All'].get_node_ids(), [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20
])
def test_get_reports_from_population(self):
self.assertEqual(self.test_obj['All'].times, (0., 4., 0.2))
# check following calls succeed (no memory destroyed)
self.assertEqual(self.test_obj['All'].times, (0., 4., 0.2))
self.assertEqual(self.test_obj['All'].time_units, 'ms')
self.assertEqual(self.test_obj['All'].data_units, 'mV')
self.assertTrue(self.test_obj['All'].sorted)
self.assertEqual(len(self.test_obj['All'].get(tstride=2).data),
10) # Number of times in this range
self.assertEqual(len(self.test_obj['All'].get(tstride=2).times),
10) # Should be the same
self.assertEqual(len(self.test_obj['All'].get().ids), 100)
sel = self.test_obj['All'].get(node_ids=[13, 14],
tstart=0.8,
tstop=1.2)
keys = list(sel.ids)
keys.sort()
self.assertEqual(keys,
[(13, 30), (13, 30), (13, 31), (13, 31), (13, 32),
(14, 32), (14, 33), (14, 33), (14, 34), (14, 34)])
self.assertEqual(len(self.test_obj['All'].get(node_ids=[]).data), 0)
self.assertEqual(len(self.test_obj['All'].get(node_ids=[]).times), 0)
self.assertEqual(len(self.test_obj['All'].get(node_ids=[]).ids), 0)
self.assertEqual(len(sel.times),
3) # Number of timestamp (0.8, 1.0 and 1.2)
with self.assertRaises(SonataError):
self.test_obj['All'].get(tstart=5.) # tstart out of range
# tstart should be <= tstop
np.testing.assert_allclose(
self.test_obj['All'].get(node_ids=[1, 2], tstart=3.,
tstop=3.).data[0], [
150.0, 150.1, 150.2, 150.3, 150.4,
150.5, 150.6, 150.7, 150.8, 150.9
])
# check following calls succeed (no memory destroyed)
np.testing.assert_allclose(
self.test_obj['All'].get(node_ids=[1, 2], tstart=3.,
tstop=3.).data[0], [
150.0, 150.1, 150.2, 150.3, 150.4,
150.5, 150.6, 150.7, 150.8, 150.9
])
np.testing.assert_allclose(
self.test_obj['All'].get(node_ids=[3, 4], tstart=0.2,
tstop=0.4).data[0],
[11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9], 1e-6,
0)
np.testing.assert_allclose(
self.test_obj['All'].get(node_ids=[3, 4], tstride=4).data[2],
[81.0, 81.1, 81.2, 81.3, 81.4, 81.5, 81.6, 81.7, 81.8, 81.9], 1e-6,
0)