def test_set_parameters_file(self):
parameter_file = os.path.join(self.output_test_dir,
self.parameter_filename)
shutil.copy(os.path.join(self.test_data_dir, self.parameter_filename),
parameter_file)
parameter_change = {
"soma gbar_nat": 10,
"basal gbar_ih": 10,
"iseg vshift2_nat": 10
}
parameter_list = [["soma gbar_nat", 284.546493, None],
["basal gbar_ih", 15.709707, None],
["iseg vshift2_nat", -9.802976, None]]
self.parameters = Parameters(parameter_list)
self.parameters.set_parameters_file(parameter_file, parameter_change)
compare_file = os.path.join(self.test_data_dir,
"example_hoc_control_parameters.hoc")
result = subprocess.call(["diff", parameter_file, compare_file])
self.assertEqual(result, 0)
def test_getitem(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
self.assertIsInstance(self.parameters["gbar_Na"], Parameter)
def test_get_error(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
with self.assertRaises(AttributeError):
self.parameters.get("not_a_parameter")
def test_ordered(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
parameter_list = [["gbar_K", 36, cp.Normal(36, 1)],
["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("value")
self.assertEqual(uncertain_parameters, [36, 120, 0.3])
def test_get_from_uncertain_distribution(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get_from_uncertain("distribution")
self.assertEqual(len(result), 2)
self.assertIsInstance(result[0], cp.Dist)
self.assertIsInstance(result[1], cp.Dist)
def test_get_from_uncertain_name(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get_from_uncertain()
self.assertIn("gbar_Na", result)
self.assertIn("gbar_K", result)
self.assertNotIn("gbar_L", result)
def test_get_value_list(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get("value", ["gbar_Na", "gbar_K"])
self.assertIn(120, result)
self.assertIn(36, result)
def test_get_distribution(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get("distribution")
self.assertEqual(len(result), 3)
self.assertIsInstance(result[0], cp.Dist)
self.assertIsInstance(result[1], cp.Dist)
self.assertIsInstance(result[2], cp.Dist)
def test_get_name(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_l", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get()
self.assertIn("gbar_Na", result)
self.assertIn("gbar_K", result)
self.assertIn("gbar_l", result)
def test_set_distribution(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
def distribution_function(x):
return cp.Uniform(x - 10, x + 10)
self.parameters.set_distribution("gbar_Na", distribution_function)
self.assertIsInstance(self.parameters["gbar_Na"].distribution,
cp.Distribution)
def test_setitem(self):
parameter = Parameter("gbar_Na", 120, cp.Uniform(110, 130))
parameters = Parameters()
parameters["gbar_Na"] = parameter
self.assertTrue("gbar_Na" in parameters.parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
def test_reset_parameter_file(self):
parameter_file = os.path.join(self.output_test_dir, self.parameter_filename)
shutil.copy(os.path.join(self.test_data_dir, self.parameter_filename),
parameter_file)
parameter_list = [["soma gbar_nat", 10, None],
["basal gbar_ih", 10, None],
["iseg vshift2_nat", 10, None]]
self.parameters = Parameters(parameter_list)
self.parameters.reset_parameter_file(parameter_file)
compare_file = os.path.join(self.test_data_dir, "example_hoc_control_parameters.hoc")
result = subprocess.call(["diff", parameter_file, compare_file])
self.assertEqual(result, 0)
def test_delitem(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
del parameters["gbar_Na"]
self.assertEqual(len(parameters.parameters), 2)
def test_str(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, cp.Uniform(0.1, 0.5)]]
parameters = Parameters(parameter_list)
result = str(parameters)
self.assertEqual(result,
"gbar_Na: 120\ngbar_K: 36\ngbar_L: 0.3 - Uncertain")
def test_init_object_dist(self):
parameter_list = [Parameter("gbar_Na", 120, cp.Uniform(110, 130)),
Parameter("gbar_K", 36),
Parameter("gbar_L", 10.3)]
parameters = Parameters(parameter_list, distribution=cp.Uniform(110, 130))
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsInstance(parameters.distribution, cp.Dist)
def test_iter(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
result = [parameter for parameter in parameters]
self.assertEqual(len(result), 3)
self.assertIsInstance(result[0], Parameter)
self.assertIsInstance(result[1], Parameter)
self.assertIsInstance(result[2], Parameter)
def test_init_list_none(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].distribution, None)
self.assertEqual(parameters["gbar_K"].distribution, None)
self.assertEqual(parameters["gbar_L"].distribution, None)
def test_init_list_only_values(self):
parameter_list = [["gbar_Na", 120], ["gbar_K", 36], ["gbar_L", 0.3]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].value, 120)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsNone(parameters["gbar_Na"].distribution)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_set_parameters(self):
base = ParameterBase()
parameter_list = [["a", 1, None], ["b", 2, None]]
base.parameters = parameter_list
self.assertIsInstance(base.parameters, Parameters)
self.assertEqual(base.parameters["a"].value, 1)
self.assertEqual(base.parameters["b"].value, 2)
parameter_list = [["a", 1, None], ["b", 2, None]]
base.parameters = Parameters(parameter_list)
self.assertIsInstance(base.parameters, Parameters)
self.assertEqual(base.parameters["a"].value, 1)
self.assertEqual(base.parameters["b"].value, 2)
def setUp(self):
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.features = TestingFeatures(features_to_run=[
"feature0d", "feature1d", "feature2d", "feature_invalid",
"feature_adaptive"
])
self.parameter_list = [["a", 1, None], ["b", 2, None]]
self.parameters = Parameters(self.parameter_list)
self.runmodel = RunModel(model=TestingModel1d(),
parameters=self.parameters,
features=self.features)
def test_init_list_chaospy(self):
parameter_list = [["gbar_Na", 120, cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].value, 120)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution, cp.Dist)
self.assertIsInstance(parameters["gbar_K"].distribution, cp.Dist)
self.assertIsInstance(parameters["gbar_L"].distribution, cp.Dist)
def test_init_list_mixed(self):
parameter_list = [["gbar_Na", cp.Uniform(110, 130)], ["gbar_K", 36],
["gbar_L", 0.3]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_init_list_only_chaospy(self):
parameter_list = [["gbar_Na", cp.Uniform(110, 130)],
["gbar_K", cp.Normal(36, 1)],
["gbar_l", cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_l"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertIsNone(parameters["gbar_K"].value)
self.assertIsNone(parameters["gbar_l"].value)
self.assertIsInstance(parameters["gbar_Na"].distribution, cp.Dist)
self.assertIsInstance(parameters["gbar_K"].distribution, cp.Dist)
self.assertIsInstance(parameters["gbar_l"].distribution, cp.Dist)
def test_init_dict(self):
parameters = {"gbar_Na": cp.Uniform(110, 130),
"gbar_K": 36,
"gbar_L": 0.3}
parameters = Parameters(parameters)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution, cp.Dist)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_init_no_list(self):
parameter_list = 1
with self.assertRaises(TypeError):
Parameters(parameter_list)
def test_init_list_to_long(self):
parameter_list = [["gbar_Na", 120, None, 1]]
with self.assertRaises(TypeError):
Parameters(parameter_list)
class TestParameters(unittest.TestCase):
def setUp(self):
self.parameter_filename = "example_hoc.hoc"
self.folder = os.path.dirname(os.path.realpath(__file__))
self.test_data_dir = os.path.join(self.folder, "data")
self.data_file = "example_hoc.hoc"
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)
def tearDown(self):
if os.path.isdir(self.output_test_dir):
shutil.rmtree(self.output_test_dir)
def test_init_list_none(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].distribution, None)
self.assertEqual(parameters["gbar_K"].distribution, None)
self.assertEqual(parameters["gbar_L"].distribution, None)
def test_init_list_chaospy(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].value, 120)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsInstance(parameters["gbar_K"].distribution,
cp.Distribution)
self.assertIsInstance(parameters["gbar_L"].distribution,
cp.Distribution)
def test_init_object(self):
parameter_list = [
Parameter("gbar_Na", 120, cp.Uniform(110, 130)),
Parameter("gbar_K", 36),
Parameter("gbar_L", 10.3)
]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters.distribution)
def test_init_object_dist(self):
parameter_list = [
Parameter("gbar_Na", 120, cp.Uniform(110, 130)),
Parameter("gbar_K", 36),
Parameter("gbar_L", 10.3)
]
parameters = Parameters(parameter_list,
distribution=cp.Uniform(110, 130))
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsInstance(parameters.distribution, cp.Distribution)
def test_init_list_only_chaospy(self):
parameter_list = [["gbar_Na", cp.Uniform(110, 130)],
["gbar_K", cp.Normal(36, 1)],
["gbar_L", cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertIsNone(parameters["gbar_K"].value)
self.assertIsNone(parameters["gbar_L"].value)
self.assertIsInstance(parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsInstance(parameters["gbar_K"].distribution,
cp.Distribution)
self.assertIsInstance(parameters["gbar_L"].distribution,
cp.Distribution)
def test_init_list_only_values(self):
parameter_list = [["gbar_Na", 120], ["gbar_K", 36], ["gbar_L", 0.3]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertEqual(parameters["gbar_Na"].value, 120)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsNone(parameters["gbar_Na"].distribution)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_init_list_mixed(self):
parameter_list = [["gbar_Na", cp.Uniform(110, 130)], ["gbar_K", 36],
["gbar_L", 0.3]]
parameters = Parameters(parameter_list)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_init_dict(self):
parameters = {
"gbar_Na": cp.Uniform(110, 130),
"gbar_K": 36,
"gbar_L": 0.3
}
parameters = Parameters(parameters)
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsNone(parameters["gbar_Na"].value)
self.assertEqual(parameters["gbar_K"].value, 36)
self.assertEqual(parameters["gbar_L"].value, 0.3)
self.assertIsInstance(parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsNone(parameters["gbar_K"].distribution)
self.assertIsNone(parameters["gbar_L"].distribution)
def test_ordered(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
parameter_list = [["gbar_K", 36, cp.Normal(36, 1)],
["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("value")
self.assertEqual(uncertain_parameters, [36, 120, 0.3])
def test_init_list_to_long(self):
parameter_list = [["gbar_Na", 120, None, 1]]
with self.assertRaises(TypeError):
Parameters(parameter_list)
def test_init_no_list(self):
parameter_list = 1
with self.assertRaises(TypeError):
Parameters(parameter_list)
def test_getitem(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
self.assertIsInstance(self.parameters["gbar_Na"], Parameter)
def test_iter(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
result = [parameter for parameter in parameters]
self.assertEqual(len(result), 3)
self.assertIsInstance(result[0], Parameter)
self.assertIsInstance(result[1], Parameter)
self.assertIsInstance(result[2], Parameter)
def test_delitem(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
del parameters["gbar_Na"]
self.assertEqual(len(parameters.parameters), 2)
def test_setitem(self):
parameter = Parameter("gbar_Na", 120, cp.Uniform(110, 130))
parameters = Parameters()
parameters["gbar_Na"] = parameter
self.assertTrue("gbar_Na" in parameters.parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
def test_set_distribution(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
def distribution_function(x):
return cp.Uniform(x - 10, x + 10)
self.parameters.set_distribution("gbar_Na", distribution_function)
self.assertIsInstance(self.parameters["gbar_Na"].distribution,
cp.Distribution)
def set_all_distributions(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
def distribution_function(x):
return cp.Uniform(x - 10, x + 10)
self.parameters.set_all_distributions(distribution_function)
self.assertIsInstance(self.parameters["gbar_Na"].distribution,
cp.Distribution)
self.assertIsInstance(self.parameters["gbar_K"].distribution,
cp.Distribution)
self.assertIsInstance(self.parameters["gbar_L"].distribution,
cp.Distribution)
def test_get_from_uncertain_name(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get_from_uncertain()
self.assertIn("gbar_Na", result)
self.assertIn("gbar_K", result)
self.assertNotIn("gbar_L", result)
def test_get_from_uncertain_value(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get_from_uncertain("value")
self.assertIn(120, result)
self.assertIn(36, result)
self.assertNotIn(0.3, result)
def test_get_from_uncertain_distribution(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, None]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get_from_uncertain("distribution")
self.assertEqual(len(result), 2)
self.assertIsInstance(result[0], cp.Distribution)
self.assertIsInstance(result[1], cp.Distribution)
def test_get_name(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get()
self.assertIn("gbar_Na", result)
self.assertIn("gbar_K", result)
self.assertIn("gbar_L", result)
def test_get_value(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get("value")
self.assertIn(120, result)
self.assertIn(36, result)
self.assertIn(0.3, result)
def test_get_value_list(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get("value", ["gbar_Na", "gbar_K"])
self.assertIn(120, result)
self.assertIn(36, result)
def test_get_error(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
with self.assertRaises(AttributeError):
self.parameters.get("not_a_parameter")
def test_get_distribution(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
self.parameters = Parameters(parameter_list)
result = self.parameters.get("distribution")
self.assertEqual(len(result), 3)
self.assertIsInstance(result[0], cp.Distribution)
self.assertIsInstance(result[1], cp.Distribution)
self.assertIsInstance(result[2], cp.Distribution)
def test_set_parameters_file(self):
parameter_file = os.path.join(self.output_test_dir,
self.parameter_filename)
shutil.copy(os.path.join(self.test_data_dir, self.parameter_filename),
parameter_file)
parameter_change = {
"soma gbar_nat": 10,
"basal gbar_ih": 10,
"iseg vshift2_nat": 10
}
parameter_list = [["soma gbar_nat", 284.546493, None],
["basal gbar_ih", 15.709707, None],
["iseg vshift2_nat", -9.802976, None]]
self.parameters = Parameters(parameter_list)
self.parameters.set_parameters_file(parameter_file, parameter_change)
compare_file = os.path.join(self.test_data_dir,
"example_hoc_control_parameters.hoc")
result = subprocess.call(["diff", parameter_file, compare_file])
self.assertEqual(result, 0)
def test_reset_parameter_file(self):
parameter_file = os.path.join(self.output_test_dir,
self.parameter_filename)
shutil.copy(os.path.join(self.test_data_dir, self.parameter_filename),
parameter_file)
parameter_list = [["soma gbar_nat", 10, None],
["basal gbar_ih", 10, None],
["iseg vshift2_nat", 10, None]]
self.parameters = Parameters(parameter_list)
self.parameters.reset_parameter_file(parameter_file)
compare_file = os.path.join(self.test_data_dir,
"example_hoc_control_parameters.hoc")
result = subprocess.call(["diff", parameter_file, compare_file])
self.assertEqual(result, 0)
def test_str(self):
parameter_list = [["gbar_Na", 120, None], ["gbar_K", 36, None],
["gbar_L", 0.3, cp.Uniform(0.1, 0.5)]]
parameters = Parameters(parameter_list)
result = str(parameters)
self.assertEqual(result,
"gbar_Na: 120\ngbar_K: 36\ngbar_L: 0.3 - Uncertain")
