class TestSOVTree():
def loadTTree(self):
'''
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
'''
print '>>> loading T-tree <<<'
fname = 'test_morphologies/Tsovtree.swc'
self.tree = SOVTree(fname, types=[1, 3, 4])
self.tree.fitLeakCurrent(e_eq_target=-75., tau_m_target=10.)
self.tree.setCompTree()
def loadValidationTree(self):
'''
Load the T-tree morphology in memory
5---1---4
'''
print '>>> loading validation tree <<<'
fname = 'test_morphologies/sovvalidationtree.swc'
self.tree = SOVTree(fname, types=[1, 3, 4])
self.tree.fitLeakCurrent(e_eq_target=-75., tau_m_target=10.)
self.tree.setCompTree()
def testSOVCalculation(self):
# validate the calculation on analytical model
self.loadValidationTree()
# do SOV calculation
self.tree.calcSOVEquations()
alphas, gammas = self.tree.getSOVMatrices([(1, 0.5)])
# compute time scales analytically
self.tree.treetype = 'computational'
lambda_m_test = np.sqrt(self.tree[4].R_sov / \
(2.*self.tree[4].g_m*self.tree[4].r_a))
tau_m_test = self.tree[4].c_m / self.tree[4].g_m * 1e3
alphas_test = \
(1. + \
(np.pi * np.arange(20) * lambda_m_test / \
(self.tree[4].L_sov + self.tree[5].L_sov))**2) / \
tau_m_test
# compare analytical and computed time scales
assert np.allclose(alphas[:20], alphas_test)
# compute the spatial mode functions analytically
# import matplotlib.pyplot as pl
# self.tree.distributeLocsUniform(dx=4., name='NET_eval')
# alphas, gammas = self.tree.getSOVMatrices(self.tree.getLocs(name='NET_eval'))
# for kk in range(5):
# print 'tau_' + str(kk) + ' =', -1./alphas[kk].real
# pl.plot(range(gammas.shape[1]), gammas[kk,:])
# pl.plot(range(gammas.shape[1]), g)
# pl.show()
## TODO
# test basic identities
self.loadTTree()
self.tree.calcSOVEquations(maxspace_freq=500)
# sets of location
locs_0 = [(6, .5), (8, .5)]
locs_1 = [(1, .5), (4, .5), (4, 1.), (5, .5), (6, .5), (7, .5),
(8, .5)]
locs_2 = [(7, .5), (8, .5)]
self.tree.storeLocs(locs_0, '0')
self.tree.storeLocs(locs_1, '1')
self.tree.storeLocs(locs_2, '2')
# test mode importance
imp_a = self.tree.getModeImportance(locs=locs_0)
imp_b = self.tree.getModeImportance(name='0')
imp_c = self.tree.getModeImportance(sov_data=self.tree.getSOVMatrices(
locs=locs_0))
imp_d = self.tree.getModeImportance(sov_data=self.tree.getSOVMatrices(
name='0'))
assert np.allclose(imp_a, imp_b)
assert np.allclose(imp_a, imp_c)
assert np.allclose(imp_a, imp_d)
assert np.abs(1. - np.max(imp_a)) < 1e-12
with pytest.raises(IOError):
self.tree.getModeImportance()
# test important modes
imp_2 = self.tree.getModeImportance(name='2')
assert not np.allclose(imp_a, imp_2)
# test impedance matrix
z_mat_a = self.tree.calcImpedanceMatrix(
sov_data=self.tree.getImportantModes(name='1', eps=1e-10))
z_mat_b = self.tree.calcImpedanceMatrix(name='1', eps=1e-10)
assert np.allclose(z_mat_a, z_mat_b)
assert np.allclose(z_mat_a - z_mat_a.T, np.zeros(z_mat_a.shape))
for ii, z_row in enumerate(z_mat_a):
assert np.argmax(z_row) == ii
# test Fourrier impedance matrix
ft = ke.FourrierTools(np.arange(0., 100., 0.1))
z_mat_ft = self.tree.calcImpedanceMatrix(name='1',
eps=1e-10,
freqs=ft.s)
print z_mat_ft[ft.ind_0s, :, :]
print z_mat_a
assert np.allclose(z_mat_ft[ft.ind_0s,:,:].real, \
z_mat_a, atol=1e-1) # check steady state
assert np.allclose(z_mat_ft - np.transpose(z_mat_ft, axes=(0,2,1)), \
np.zeros(z_mat_ft.shape)) # check symmetry
assert np.allclose(z_mat_ft[:ft.ind_0s,:,:].real, \
z_mat_ft[ft.ind_0s+1:,:,:][::-1,:,:].real) # check real part even
assert np.allclose(z_mat_ft[:ft.ind_0s,:,:].imag, \
-z_mat_ft[ft.ind_0s+1:,:,:][::-1,:,:].imag) # check imaginary part odd
# import matplotlib.pyplot as pl
# pl.plot(ft.s.imag, z_mat_ft[:,2,4].real, 'b')
# pl.plot(ft.s.imag, z_mat_ft[:,2,4].imag, 'r')
# pl.show()
# self.tree.distributeLocsUniform(dx=4., name='NET_eval')
# print [str(loc) for loc in self.tree.getLocs(name='NET_eval')]
# z_m = self.tree.calcImpedanceMatrix(name='NET_eval', eps=1e-10)
# pl.imshow(z_m, origin='lower', interpolation='none')
# alphas, gammas = self.tree.getSOVMatrices(self.tree.getLocs(name='NET_eval'))
# for kk in range(5):
# print 'tau_' + str(kk) + ' =', -1./alphas[kk].real
# pl.plot(range(gammas.shape[1]), gammas[kk,:])
# pl.show()
# import morphologyReader as morphR
def testNETDerivation(self):
# initialize
self.loadValidationTree()
self.tree.calcSOVEquations()
# construct the NET
net = self.tree.constructNET()
# print str(net)
# initialize
self.loadTTree()
self.tree.calcSOVEquations()
# construct the NET
net = self.tree.constructNET(dz=20.)
# print str(net)
# contruct the NET with linear terms
net, lin_terms = self.tree.constructNET(dz=20., add_lin_terms=True)
# check if correct
alphas, gammas = self.tree.getImportantModes(name='NET_eval',
eps=1e-4,
sort_type='timescale')
for ii, lin_term in enumerate(lin_terms):
z_k_trans = net.getReducedTree([0, ii
]).getRoot().z_kernel + lin_term
assert np.abs(z_k_trans.k_bar - Kernel(
(alphas, gammas[:, 0] * gammas[:, ii])).k_bar) < 1e-8
class TestSOVTree():
def loadTTree(self):
"""
Load the T-tree morphology in memory
6--5--4--7--8
|
|
1
"""
fname = os.path.join(MORPHOLOGIES_PATH_PREFIX, 'Tsovtree.swc')
self.tree = SOVTree(fname, types=[1,3,4])
self.tree.fitLeakCurrent(-75., 10.)
self.tree.setCompTree()
def loadValidationTree(self):
"""
Load the T-tree morphology in memory
5---1---4
"""
fname = os.path.join(MORPHOLOGIES_PATH_PREFIX, 'sovvalidationtree.swc')
self.tree = SOVTree(fname, types=[1,3,4])
self.tree.fitLeakCurrent(-75., 10.)
self.tree.setCompTree()
def testSOVCalculation(self):
# validate the calculation on analytical model
self.loadValidationTree()
# do SOV calculation
self.tree.calcSOVEquations()
alphas, gammas = self.tree.getSOVMatrices([(1, 0.5)])
# compute time scales analytically
self.tree.treetype = 'computational'
lambda_m_test = np.sqrt(self.tree[4].R_sov / \
(2.*self.tree[4].g_m*self.tree[4].r_a))
tau_m_test = self.tree[4].c_m / self.tree[4].g_m * 1e3
alphas_test = \
(1. + \
(np.pi * np.arange(20) * lambda_m_test / \
(self.tree[4].L_sov + self.tree[5].L_sov))**2) / \
tau_m_test
# compare analytical and computed time scales
assert np.allclose(alphas[:20], alphas_test)
# compute the spatial mode functions analytically
## TODO
# test basic identities
self.loadTTree()
self.tree.calcSOVEquations(maxspace_freq=500)
# sets of location
locs_0 = [(6, .5), (8, .5)]
locs_1 = [(1, .5), (4, .5), (4, 1.), (5, .5), (6, .5), (7, .5), (8, .5)]
locs_2 = [(7, .5), (8, .5)]
self.tree.storeLocs(locs_0, '0')
self.tree.storeLocs(locs_1, '1')
self.tree.storeLocs(locs_2, '2')
# test mode importance
imp_a = self.tree.getModeImportance(locarg=locs_0)
imp_b = self.tree.getModeImportance(locarg='0')
imp_c = self.tree.getModeImportance(
sov_data=self.tree.getSOVMatrices(locarg=locs_0))
imp_d = self.tree.getModeImportance(
sov_data=self.tree.getSOVMatrices(locarg='0'))
assert np.allclose(imp_a, imp_b)
assert np.allclose(imp_a, imp_c)
assert np.allclose(imp_a, imp_d)
assert np.abs(1. - np.max(imp_a)) < 1e-12
with pytest.raises(IOError):
self.tree.getModeImportance()
# test important modes
imp_2 = self.tree.getModeImportance(locarg='2')
assert not np.allclose(imp_a, imp_2)
# test impedance matrix
z_mat_a = self.tree.calcImpedanceMatrix(
sov_data=self.tree.getImportantModes(locarg='1', eps=1e-10))
z_mat_b = self.tree.calcImpedanceMatrix(locarg='1', eps=1e-10)
assert np.allclose(z_mat_a, z_mat_b)
assert np.allclose(z_mat_a - z_mat_a.T, np.zeros(z_mat_a.shape))
for ii, z_row in enumerate(z_mat_a):
assert np.argmax(z_row) == ii
# test Fourrier impedance matrix
ft = ke.FourrierTools(np.arange(0.,100.,0.1))
z_mat_ft = self.tree.calcImpedanceMatrix(locarg='1', eps=1e-10, freqs=ft.s)
assert np.allclose(z_mat_ft[ft.ind_0s,:,:].real, \
z_mat_a, atol=1e-1) # check steady state
assert np.allclose(z_mat_ft - np.transpose(z_mat_ft, axes=(0,2,1)), \
np.zeros(z_mat_ft.shape)) # check symmetry
assert np.allclose(z_mat_ft[:ft.ind_0s,:,:].real, \
z_mat_ft[ft.ind_0s+1:,:,:][::-1,:,:].real) # check real part even
assert np.allclose(z_mat_ft[:ft.ind_0s,:,:].imag, \
-z_mat_ft[ft.ind_0s+1:,:,:][::-1,:,:].imag) # check imaginary part odd
def loadBall(self):
"""
Load point neuron model
"""
fname = os.path.join(MORPHOLOGIES_PATH_PREFIX, 'ball.swc')
self.btree = SOVTree(fname, types=[1,3,4])
self.btree.fitLeakCurrent(-75., 10.)
self.btree.setCompTree()
def testSingleCompartment(self):
self.loadBall()
# for validation
greenstree = self.btree.__copy__(new_tree=GreensTree())
greenstree.setCompTree()
greenstree.setImpedance(np.array([0.]))
z_inp = greenstree.calcImpedanceMatrix([(1.,0.5)])
self.btree.calcSOVEquations(maxspace_freq=500)
alphas, gammas = self.btree.getSOVMatrices(locarg=[(1.,.5)])
z_inp_sov = self.btree.calcImpedanceMatrix(locarg=[(1.,.5)])
assert alphas.shape[0] == 1
assert gammas.shape == (1,1)
assert np.abs(1./np.abs(alphas[0]) - 10.) < 1e-10
g_m = self.btree[1].getGTot(self.btree.channel_storage)
g_s = g_m * 4.*np.pi*(self.btree[1].R*1e-4)**2
assert np.abs(gammas[0,0]**2/np.abs(alphas[0]) - 1./g_s) < 1e-10
assert np.abs(z_inp_sov - 1./g_s) < 1e-10
def testNETDerivation(self):
# initialize
self.loadValidationTree()
self.tree.calcSOVEquations()
# construct the NET
net = self.tree.constructNET()
# initialize
self.loadTTree()
self.tree.calcSOVEquations()
# construct the NET
net = self.tree.constructNET(dz=20.)
# contruct the NET with linear terms
net, lin_terms = self.tree.constructNET(dz=20., add_lin_terms=True)
# check if correct
alphas, gammas = self.tree.getImportantModes(locarg='net eval',
eps=1e-4, sort_type='timescale')
for ii, lin_term in lin_terms.items():
z_k_trans = net.getReducedTree([0,ii]).getRoot().z_kernel + lin_term
assert np.abs(z_k_trans.k_bar - Kernel((alphas, gammas[:,0]*gammas[:,ii])).k_bar) < 1e-8