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')
def setUp(self):
self.population = NodeStorage(os.path.join(
PATH, 'nodes1.h5')).open_population('nodes-A')
class TestNodePopulationNodeSet(unittest.TestCase):
def setUp(self):
self.population = NodeStorage(os.path.join(
PATH, 'nodes1.h5')).open_population('nodes-A')
def test_BasicScalarInt(self):
sel = NodeSets('{ "NodeSet0": { "attr-Y": 21 } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, Selection(((0, 1), )))
def test_BasicScalarString(self):
sel = NodeSets(
'{ "NodeSet0": { "attr-Z": ["aa", "cc"] } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, Selection(((0, 1), (2, 3))))
def test_BasicScalarEnum(self):
sel = NodeSets(
'{ "NodeSet0": { "E-mapping-good": "C" } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, Selection((
(0, 1),
(2, 3),
(4, 6),
)))
def test_BasicScalarAnded(self):
j = '''{"NodeSet0": {"E-mapping-good": "C",
"attr-Y": [21, 22]
}
}'''
sel = NodeSets(j).materialize("NodeSet0", self.population)
self.assertEqual(sel, Selection(((0, 1), )))
def test_BasicScalarNodeId(self):
sel = NodeSets('{ "NodeSet0": { "node_id": [1, 3, 5] } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, Selection(((1, 2), (3, 4), (5, 6))))
def test_BasicScalarPopulation(self):
sel = NodeSets(
'{ "NodeSet0": { "population": "nodes-A" } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, self.population.select_all())
sel = NodeSets('{ "NodeSet0": { "population": ["nodes-A", "FAKE"] } }'
).materialize("NodeSet0", self.population)
self.assertEqual(sel, self.population.select_all())
sel = NodeSets(
'{ "NodeSet0": { "population": "NOT_A_POP" } }').materialize(
"NodeSet0", self.population)
self.assertEqual(sel, Selection([]))
def test_NodeSetCompound(self):
j = '''{"NodeSet0": { "node_id": [1] },
"NodeSet1": { "node_id": [2] },
"NodeSetCompound0": ["NodeSet0", "NodeSet1"],
"NodeSetCompound1": ["NodeSetCompound0", "NodeSet2"],
"NodeSet2": { "node_id": [3] }
}'''
sel = NodeSets(j).materialize("NodeSetCompound1", self.population)
self.assertEqual(sel, Selection(((1, 4), )))
def test_NodeSet_toJSON(self):
j = '''
{"bio_layer45": {
"model_type": "biophysical",
"location": ["layer4", "layer5"]
},
"V1_point_prime": {
"population": "biophysical",
"model_type": "point",
"node_id": [1, 2, 3, 5, 7, 9]
},
"combined": ["bio_layer45", "V1_point_prime"]
}'''
new = NodeSets(j).toJSON()
ns1 = NodeSets(new)
self.assertEqual(new, ns1.toJSON())
ns = NodeSets.from_file(os.path.join(PATH, 'node_sets.json'))
self.assertEqual(new, ns.toJSON())
def setUp(self):
path = os.path.join(PATH, 'nodes1.h5')
self.test_obj = NodeStorage(path).open_population('nodes-A')
class TestNodePopulation(unittest.TestCase):
def setUp(self):
path = os.path.join(PATH, 'nodes1.h5')
self.test_obj = NodeStorage(path).open_population('nodes-A')
def test_name(self):
self.assertEqual(self.test_obj.name, "nodes-A")
def test_size(self):
self.assertEqual(self.test_obj.size, 6)
self.assertEqual(len(self.test_obj), 6)
def test_attribute_names(self):
self.assertEqual(
self.test_obj.attribute_names, {
'attr-X', 'attr-Y', 'attr-Z', 'A-int8', 'A-int16', 'A-int32',
'A-int64', 'A-uint8', 'A-uint16', 'A-uint32', 'A-uint64',
'A-float', 'A-double', 'A-string', 'A-enum', 'E-mapping-good',
'E-mapping-bad'
})
def test_get_attribute(self):
self.assertEqual(self.test_obj.get_attribute('attr-X', 0), 11.)
self.assertEqual(
self.test_obj.get_attribute('attr-X', Selection([0, 5])).tolist(),
[11., 16.])
# different dtypes
self.assertEqual(self.test_obj.get_attribute('attr-Y', 0), 21)
self.assertEqual(self.test_obj.get_attribute('attr-Z', 0), 'aa')
# default value
self.assertEqual(
self.test_obj.get_attribute('attr-X', Selection([0, 5]),
42.).tolist(), [11., 16.])
self.assertRaises(SonataError, self.test_obj.get_attribute,
'no-such-attribute', 0)
def test_get_dynamics_attribute(self):
self.assertEqual(self.test_obj.get_dynamics_attribute('dparam-X', 0),
1011.)
self.assertEqual(
self.test_obj.get_dynamics_attribute('dparam-X',
Selection([0, 5])).tolist(),
[1011., 1016.])
# different dtypes
self.assertEqual(self.test_obj.get_dynamics_attribute('dparam-Y', 0),
1021)
self.assertEqual(self.test_obj.get_dynamics_attribute('dparam-Z', 0),
'd-aa')
# default value
self.assertEqual(
self.test_obj.get_dynamics_attribute('dparam-X', Selection([0, 5]),
42.).tolist(), [1011., 1016.])
self.assertRaises(SonataError, self.test_obj.get_dynamics_attribute,
'no-such-attribute', 0)
def test_enumeration_names(self):
self.assertEqual(self.test_obj.enumeration_names,
{'E-mapping-good', 'E-mapping-bad'})
def test_enumeration_values(self):
self.assertEqual(
self.test_obj.get_attribute("E-mapping-good",
Selection([(0, 1), (2, 3)])).tolist(),
["C", "C"])
self.assertEqual(
self.test_obj.get_attribute("E-mapping-good",
Selection([(0, 1), (2, 3)])).tolist(),
["C", "C"])
self.assertEqual(
self.test_obj.get_enumeration("E-mapping-good",
Selection([(0, 1),
(2, 3)])).tolist(),
[2, 2])
self.assertEqual(self.test_obj.enumeration_values("E-mapping-good"),
["A", "B", "C"])
self.assertRaises(SonataError, self.test_obj.get_attribute,
"E-mapping-bad", 1)
self.assertRaises(SonataError, self.test_obj.get_enumeration, "attr-X",
0)
def test_select_all(self):
self.assertEqual(self.test_obj.select_all().flat_size, 6)
def test_match_values(self):
# string
self.assertEqual(
self.test_obj.match_values("attr-Z", "bb").flatten().tolist(), [1])
# enum
self.assertEqual(
self.test_obj.match_values("E-mapping-good",
"C").flatten().tolist(), [0, 2, 4, 5])
# int
self.assertEqual(
self.test_obj.match_values("attr-Y", 23).flatten().tolist(), [
2,
])
# float
self.assertRaises(TypeError, self.test_obj.match_values, "attr-Y", 23.)