def test_parameter_arithmetic(self):
"""Test parameter arithmetic"""
p1 = nest.CreateParameter('constant', {'value': 3.0})
p2 = nest.CreateParameter('constant', {'value': 2.0})
self.assertEqual((p1 + p2).GetValue(), 5.0)
self.assertEqual((p1 - p2).GetValue(), 1.0)
self.assertEqual((p1 / p2).GetValue(), 1.5)
self.assertEqual((p1 * p2).GetValue(), 6.0)
def test_power_parameter(self):
"""Test parameter raised to the power of an exponent"""
# Negative values
for value in np.linspace(-5.0, 0.0, 15):
p = nest.CreateParameter('constant', {'value': value})
# Exponents must be integers
for exponent in range(-15, 15):
self.assertEqual((p**exponent).GetValue(), value**exponent)
# Positive values
for value in np.linspace(0.0, 5.0, 15):
p = nest.CreateParameter('constant', {'value': value})
for exponent in np.linspace(-5.0, 5.0, 15):
self.assertEqual((p**exponent).GetValue(), value**exponent)
def test_max_parameter(self):
"""Test max of parameter"""
reference_value = 2.0
for value in np.linspace(-5.0, 5.0, 21):
p = nest.CreateParameter('constant', {'value': value})
self.assertEqual(
nest.math.max(p, reference_value).GetValue(),
np.maximum(value, reference_value))
def test_parameter_comparison(self):
"""Test comparison of parameters"""
p1 = nest.CreateParameter('constant', {'value': 1.0})
p2 = nest.CreateParameter('constant', {'value': 2.0})
self.assertTrue((p1 < p2).GetValue())
self.assertTrue((p1 <= p2).GetValue())
self.assertTrue((p1 == p2 - p1).GetValue())
self.assertTrue((p1 != p2).GetValue())
self.assertTrue((p2 >= p1).GetValue())
self.assertTrue((p2 > p1).GetValue())
self.assertFalse((p2 < p1).GetValue())
self.assertFalse((p2 <= p1).GetValue())
self.assertFalse((p1 == p2).GetValue())
self.assertFalse((p1 != p2 - p1).GetValue())
self.assertFalse((p1 >= p2).GetValue())
self.assertFalse((p1 > p2).GetValue())
def test_syn_spec_parameter(self):
"""Test parameter in syn_spec"""
n = nest.Create('iaf_psc_alpha', 2)
p = nest.CreateParameter('constant', {'value': 2.0})
nest.Connect(n, n, syn_spec={'weight': p})
conns = nest.GetConnections()
weights = conns.get('weight')
for w in weights:
self.assertEqual(w, 2.0)
def test_conn_spec_parameter(self):
"""Test parameter in conn_spec"""
p = nest.CreateParameter('constant', {'value': 1.0})
p2 = nest.CreateParameter('constant', {'value': 2.0})
rule_specs = {
'pairwise_bernoulli': [
['p', p],
],
'fixed_outdegree': [
['outdegree', p2],
],
'fixed_indegree': [
['indegree', p2],
]
}
for rule, specs_list in rule_specs.items():
for specs in specs_list:
nest.ResetKernel()
n = nest.Create('iaf_psc_alpha', 2)
param, p = specs
nest.Connect(n, n, conn_spec={'rule': rule, param: p})
self.assertEqual(nest.num_connections, 4, f'Error with {rule}')
def test_parameter_is_spatial(self):
"""Test parameter is_spatial function"""
constant_parameter = nest.CreateParameter('constant', {'value': 1.0})
spatial_parameters = [
nest.spatial.pos.x, nest.spatial.distance, nest.spatial.distance.x
]
non_spatial_parameters = [
constant_parameter,
nest.random.uniform(),
nest.random.normal(),
nest.random.lognormal(),
nest.random.exponential()
]
def apply_assert(assert_func, p):
assert_func(p.is_spatial())
assert_func(nest.math.cos(p).is_spatial())
assert_func(nest.math.sin(p).is_spatial())
assert_func(nest.math.exp(p).is_spatial())
assert_func(nest.math.max(p, 1.0).is_spatial())
assert_func(nest.math.min(p, 1.0).is_spatial())
assert_func(nest.math.redraw(p, 0.0, 1.0).is_spatial())
assert_func((p + constant_parameter).is_spatial())
assert_func((constant_parameter + p).is_spatial())
assert_func(
nest.logic.conditional(p, constant_parameter,
constant_parameter).is_spatial())
assert_func(
nest.logic.conditional(constant_parameter, p,
constant_parameter).is_spatial())
assert_func(
nest.logic.conditional(constant_parameter, constant_parameter,
p).is_spatial())
for p in spatial_parameters:
apply_assert(self.assertTrue, p)
for p in non_spatial_parameters:
apply_assert(self.assertFalse, p)
def __init__(self,
seed,
dim,
L,
N,
spatial_distribution,
distribution_params=None,
open_bc=False,
x0=0.,
y0=0.):
"""
Construct a test object.
Parameters
----------
seed : Random seed for test
dim : Dimensions (2 or 3)
L : Side length of area / volume.
N : Number of nodes.
spatial_distribution : Name of spatial distribution to use.
distribution_params : Dict with params to update.
open_bc : Network with open boundary conditions
x0, y0 : Location of source neuron; open_bc only
Note
----
For each new distribution to be added, the following needs to be
defined:
self._<distribution> : function implementing distribution function
spatial_distributions entry : mapping distribution name to distribution function
default_params : default set of parameters for distribution
"""
if dim != 2 and open_bc:
raise ValueError("open_bc only supported for 2D")
self._seed = seed
self._dimensions = dim
self._L = float(L)
self._N = N
self._open_bc = open_bc
self._x_d, self._y_d = x0, y0
if (self._dimensions == 2):
if (self._open_bc):
self._max_dist = self._L * math.sqrt(2)
self._pdf = self._pdf_2d_obc
else:
self._max_dist = self._L / math.sqrt(2)
self._pdf = self._pdf_2d
elif (self._dimensions == 3):
self._max_dist = self._L * math.sqrt(3) / 2
self._pdf = self._pdf_3d
self._target_dists = None
self._all_dists = None
spatial_distributions = {
'constant': self._constant,
'linear': self._linear,
'exponential': self._exponential,
'gaussian': self._gauss,
'gamma': self._gamma
}
self._distribution = spatial_distributions[spatial_distribution]
default_params = {
'constant': 1.,
'linear': {
'a': -math.sqrt(2) / self._L,
'c': 1.0
},
'exponential': {
'a': 1.0,
'c': 0.0,
'tau': -self._L / (math.sqrt(2) * math.log((.1 - 0) / 1))
},
'gaussian': {
'p_center': 1.,
'sigma': self._L / 4.,
'mean': 0.,
'c': 0.
},
'gamma': {
'kappa': 3.,
'theta': self._L / 4.
}
}
self._params = default_params[spatial_distribution]
if distribution_params is not None:
if spatial_distribution == 'constant':
self._params = distribution_params
else:
self._params.update(distribution_params)
# Pre-calculate constant variables for efficiency
self._calculate_constants(spatial_distribution)
if self._dimensions == 3:
maskdict = {
'box': {
'lower_left': [-self._L / 2.] * 3,
'upper_right': [self._L / 2.] * 3
}
}
elif self._dimensions == 2 and not self._open_bc:
maskdict = {
'rectangular': {
'lower_left': [-self._L / 2.] * 2,
'upper_right': [self._L / 2.] * 2
}
}
elif self._dimensions == 2 and self._open_bc:
maskdict = {
'rectangular': {
'lower_left': [-self._L] * 2,
'upper_right': [self._L] * 2
}
}
if spatial_distribution == 'constant':
distribution = nest.CreateParameter('constant',
{'value': self._params})
elif spatial_distribution == 'linear':
distribution = self._params[
'c'] + self._params['a'] * nest.spatial.distance
elif spatial_distribution == 'exponential':
distribution = self._params[
'c'] + nest.spatial_distributions.exponential(
nest.spatial.distance, beta=self._params['tau'])
elif spatial_distribution == 'gaussian':
distribution = self._params[
'c'] + nest.spatial_distributions.gaussian(
nest.spatial.distance,
mean=self._params['mean'],
std=self._params['sigma'])
elif spatial_distribution == 'gamma':
distribution = nest.spatial_distributions.gamma(
nest.spatial.distance,
kappa=self._params['kappa'],
theta=self._params['theta'])
self._conndict = {
'rule': 'pairwise_bernoulli',
'p': distribution,
'mask': maskdict
}
def __init__(self,
seed,
dim,
L,
N,
kernel_name,
kernel_params=None,
open_bc=False,
x0=0.,
y0=0.):
'''
Construct a test object.
Parameters
----------
seed : Random seed for test
dim : Dimensions (2 or 3)
L : Side length of area / volume.
N : Number of nodes.
kernel_name : Name of kernel to use.
kernel_params: Dict with params to update.
open_bc : Network with open boundary conditions
x0, y0 : Location of source neuron; open_bc only
Note
----
For each new kernel to be added, the following needs to be
defined:
self._<kernel> : lambda-function implementing kernel function
kernels entry : mapping kernel name to kernel function
default_params : default set of parameters for kernel
'''
if dim != 2 and open_bc:
raise ValueError("open_bc only supported for 2D")
self._seed = seed
self._dimensions = dim
self._L = float(L)
self._N = N
self._open_bc = open_bc
self._x_d, self._y_d = x0, y0
if (self._dimensions == 2):
if (self._open_bc):
self._max_dist = self._L * math.sqrt(2)
else:
self._max_dist = self._L / math.sqrt(2)
elif (self._dimensions == 3):
self._max_dist = self._L * math.sqrt(3) / 2
self._target_dists = None
self._all_dists = None
# kernel functions
self._constant = lambda D: self._params
self._linear = lambda D: self._params['c'] + self._params['a'] * D
self._exponential = lambda D: (self._params['c'] + self._params['a'] *
math.exp(-D / self._params['tau']))
self._gauss = lambda D: (self._params['c'] + self._params['p_center'] *
math.exp(-(D - self._params['mean'])**2 /
(2. * self._params['sigma']**2)))
self._gamma = lambda D: (D**(self._params['kappa'] - 1) / (
self._params['theta']**self._params['kappa'] * scipy.special.gamma(
self._params['kappa'])) * math.exp(-D / self._params['theta']))
kernels = {
'constant': self._constant,
'linear': self._linear,
'exponential': self._exponential,
'gaussian': self._gauss,
'gamma': self._gamma
}
self._kernel = kernels[kernel_name]
default_params = {
'constant': 1.,
'linear': {
'a': -math.sqrt(2) / self._L,
'c': 1.0
},
'exponential': {
'a': 1.0,
'c': 0.0,
'tau': -self._L / (math.sqrt(2) * math.log((.1 - 0) / 1))
},
'gaussian': {
'p_center': 1.,
'sigma': self._L / 4.,
'mean': 0.,
'c': 0.
},
'gamma': {
'kappa': 3.,
'theta': self._L / 4.
}
}
self._params = default_params[kernel_name]
if kernel_params is not None:
if kernel_name == 'constant':
self._params = kernel_params
else:
self._params.update(kernel_params)
if self._dimensions == 3:
maskdict = {
'box': {
'lower_left': [-self._L / 2.] * 3,
'upper_right': [self._L / 2.] * 3
}
}
elif self._dimensions == 2 and not self._open_bc:
maskdict = {
'rectangular': {
'lower_left': [-self._L / 2.] * 2,
'upper_right': [self._L / 2.] * 2
}
}
elif self._dimensions == 2 and self._open_bc:
maskdict = {
'rectangular': {
'lower_left': [-self._L] * 2,
'upper_right': [self._L] * 2
}
}
if kernel_name == 'constant':
kernel = nest.CreateParameter('constant', {'value': self._params})
elif kernel_name == 'linear':
kernel = (self._params['c'] +
self._params['a'] * nest.spatial.distance)
elif kernel_name == 'exponential':
kernel = self._params['c'] + nest.spatial_distributions.exponential(
nest.spatial.distance, beta=self._params['tau'])
elif kernel_name == 'gaussian':
kernel = self._params['c'] + nest.spatial_distributions.gaussian(
nest.spatial.distance,
mean=self._params['mean'],
std=self._params['sigma'])
elif kernel_name == 'gamma':
kernel = nest.spatial_distributions.gamma(
nest.spatial.distance,
kappa=self._params['kappa'],
theta=self._params['theta'])
self._conndict = {
'rule': 'pairwise_bernoulli',
'p': kernel,
'mask': maskdict
}
def test_sin_parameter(self):
"""Test sine of a parameter"""
for value in np.linspace(-5.0, 5.0, 15):
p = nest.CreateParameter('constant', {'value': value})
self.assertAlmostEqual(nest.math.sin(p).GetValue(), np.sin(value))
def test_exp_parameter(self):
"""Test exponential of a parameter"""
for value in np.linspace(-5.0, 5.0, 15):
p = nest.CreateParameter('constant', {'value': value})
self.assertEqual(nest.math.exp(p).GetValue(), np.exp(value))