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unittest_spatial.py
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unittest_spatial.py
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'''
@author: Daniel Hjertholm
Unittests for 2D and 3D spatially structured networks.
'''
import unittest
import scipy.stats
from nest_spatial import Spatial2DTester, Spatial3DTester
class ConnectLayersTestCase(unittest.TestCase):
'''Statistical tests for ConnectLayers.'''
def setUp(self):
'''Set test parameters and critical values.'''
self.N = 100000 # Number of nodes
self.L = 1.0 # Layer size.
self.n_runs = 100 # Number of times to repeat test
# Critical values
self.alpha1 = 0.01
self.alpha2 = 0.01
def ks_test(self, tester_class, kernel_name, kernel_params={}):
'''
Create a single network using ConnectLayers, and perform a
Kolmogorov-Smirnov (KS) test on the distribution of source-target
distances. If the result is suspicious, the test is repeated n_runs
times, and the resulting p-values are compared with the expected uniform
distribution using the KS test.
Parameters
----------
tester_class : ConnectLayers2D_tester or ConnectLayers3D_tester.
kernel_name : Name of distance dependent probability
function (kernel) to test.
kernel_params: Parameters for kernel function. Optional.
Return values
-------------
boolean value. True if test was passed, False otherwise.
'''
test = tester_class(L=self.L, N=self.N, kernel_name=kernel_name,
kernel_params=kernel_params)
ks, p = test.ks_test()
if p > self.alpha1:
return True
else:
ps = []
print ''
for i in range(self.n_runs):
print 'Running test %d of %d.' % (i + 1, self.n_runs)
test = tester_class(L=self.L, N=self.N, kernel_name=kernel_name,
kernel_params=kernel_params,
seed=None)
ps.append(test.ks_test()[1])
ks, p = scipy.stats.kstest(ps, 'uniform', alternative='two_sided')
return True if p > self.alpha2 else False
def z_test(self, tester_class, kernel_name, kernel_params={}):
'''
Create a single network using ConnectLayers, and perform a Z-test on the
total connection count. If the result is suspicious, the test is
repeated n_runs times, and the resulting p-values are compared with the
expected uniform distribution using the KS test.
Parameters
----------
tester_class : ConnectLayers2D_tester or ConnectLayers3D_tester.
kernel_name : Name of distance dependent probability
function (kernel) to test.
kernel_params: Parameters for kernel function. Optional.
Return values
-------------
boolean value. True if test was passed, False otherwise.
'''
test = tester_class(L=self.L, N=self.N, kernel_name=kernel_name,
kernel_params=kernel_params)
z, p = test.z_test()
if p > self.alpha1:
return True
else:
ps = []
print ''
for i in range(self.n_runs):
print 'Running test %d of %d.' % (i + 1, self.n_runs)
test = tester_class(L=self.L, N=self.N,
kernel_name=kernel_name,
kernel_params=kernel_params,
seed=None)
ps.append(test.z_test()[1])
z, p = scipy.stats.kstest(ps, 'uniform', alternative='two_sided')
return True if p > self.alpha2 else False
def test_2D_constant_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial2DTester, 'constant',
kernel_params=0.5),
'ConnectLayers failed to pass the KS test.')
def test_2D_constant_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial3DTester, 'constant',
kernel_params=0.5),
'ConnectLayers failed to pass the Z-test')
def test_2D_linear_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial2DTester, 'linear'),
'ConnectLayers failed to pass the KS test.')
def test_2D_linear_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial2DTester, 'linear'),
'ConnectLayers failed to pass the Z-test')
def test_2D_exponential_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial2DTester, 'exponential'),
'ConnectLayers failed to pass the KS test.')
def test_2D_exponential_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial2DTester, 'exponential'),
'ConnectLayers failed to pass the Z-test')
def test_2D_gaussian_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial2DTester, 'gaussian'),
'ConnectLayers failed to pass the KS test.')
def test_2D_gaussian_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial2DTester, 'gaussian'),
'ConnectLayers failed to pass the Z-test')
def test_3D_constant_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial3DTester, 'constant',
kernel_params=0.5),
'ConnectLayers failed to pass the KS test.')
def test_3D_constant_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial3DTester, 'constant',
kernel_params=0.5),
'ConnectLayers failed to pass the Z-test')
def test_3D_linear_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial3DTester, 'linear'),
'ConnectLayers failed to pass the KS test.')
def test_3D_linear_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial3DTester, 'linear'),
'ConnectLayers failed to pass the Z-test')
def test_3D_exponential_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial3DTester, 'exponential'),
'ConnectLayers failed to pass the KS test.')
def test_3D_exponential_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial3DTester, 'exponential'),
'ConnectLayers failed to pass the Z-test')
def test_3D_gaussian_ks(self):
'''KS test performed on source-target node distances'''
self.assertTrue(self.ks_test(Spatial3DTester, 'gaussian'),
'ConnectLayers failed to pass the KS test.')
def test_3D_gaussian_z(self):
'''Z-test performed on total connection count'''
self.assertTrue(self.z_test(Spatial3DTester, 'gaussian'),
'ConnectLayers failed to pass the Z-test')
def suite():
suite = unittest.makeSuite(ConnectLayersTestCase, 'test')
return suite
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
runner.run(suite())