class Test_diff_tensor(TestCase):
"""Unit tests for the data.diff_tensor relax module."""
def calc_spheroid_objects(self, tm, Da, theta, phi):
"""Function for calculating the spheroidal diffusion tensor objects."""
# The parameter values.
Diso = 1/(6*tm)
Dpar = Diso + 2.0/3.0 * Da
Dper = Diso - 1.0/3.0 * Da
Dratio = Dpar / Dper
# Vectors.
Dpar_unit = array([sin(theta) * cos(phi), sin(theta) * sin(phi), cos(theta)])
# Matrices.
if Dpar > Dper:
axis = array([0, 0, 1], float64)
tensor_diag = array([[ Dper, 0.0, 0.0],
[ 0.0, Dper, 0.0],
[ 0.0, 0.0, Dpar]])
else:
axis = array([1, 0, 0], float64)
tensor_diag = array([[ Dpar, 0.0, 0.0],
[ 0.0, Dper, 0.0],
[ 0.0, 0.0, Dper]])
# The rotation.
rotation = zeros((3, 3), float64)
two_vect_to_R(Dpar_unit, axis, rotation)
# The diffusion tensor.
tensor = dot(rotation, dot(tensor_diag, transpose(rotation)))
# Return the objects.
return Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor
def setUp(self):
"""Set 'self.diff_data' to an empty instance of the DiffTensorData class."""
self.diff_data = DiffTensorData()
def test_append_spheroid_sim(self):
"""Test the appending of Monte Carlo simulation spheroidal diffusion tensor parameters.
The following parameters will be appended to empty lists:
- tm: 8 ns
- Da: -1e7
- theta: 150 degrees
- phi: 30 degrees
"""
# The MC sim parameter values.
tm = 8e-9
Da = -1e7
theta = (150 / 360.0) * 2.0 * pi
phi = (30 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='oblate')
# Set the number of MC sims.
self.diff_data.set_sim_num(1)
# Set the initial values.
self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0)
self.diff_data.set(param='theta', value=theta, category='sim', sim_index=0)
self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_sim[0], tm)
self.assertEqual(self.diff_data.Da_sim[0], Da)
self.assertEqual(self.diff_data.theta_sim[0], theta)
self.assertEqual(self.diff_data.phi_sim[0], phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_sim[0], Diso)
self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
self.assertEqual(self.diff_data.Dper_sim[0], Dper)
self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(), Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(), tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation_sim[0].tostring(), rotation.tostring())
self.assertEqual(self.diff_data.tensor_sim[0].tostring(), tensor.tostring())
def test_display(self):
"""Test that the contents of the diffusion tensor object can be displayed."""
print(self.diff_data)
def test_set_Diso(self):
"""Test that the Diso parameter cannot be set."""
# Assert that a RelaxError occurs when Diso is set (to the tm value of 10 ns).
self.assertRaises(RelaxError, setattr, self.diff_data, 'Diso', 1/(6*1e-8))
# Make sure that the Diso parameter has not been set.
self.assert_(not hasattr(self.diff_data, 'Diso'))
def test_set_spheroid_errors(self):
"""Test the setting of spheroidal diffusion tensor parameter errors.
The following parameter errors will be set:
- tm: 1 ns
- Da: 1e3
- theta: 3 degrees
- phi: 5 degrees
"""
# The parameter errors.
tm = 1e-8
Da = 1e3
theta = (3 / 360.0) * 2.0 * pi
phi = (5 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the diffusion parameter errors.
self.diff_data.set(param='tm', value=tm, category='err')
self.diff_data.set(param='Da', value=Da, category='err')
self.diff_data.set(param='theta', value=theta, category='err')
self.diff_data.set(param='phi', value=phi, category='err')
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_err, tm)
self.assertEqual(self.diff_data.Da_err, Da)
self.assertEqual(self.diff_data.theta_err, theta)
self.assertEqual(self.diff_data.phi_err, phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_err, Diso)
self.assertEqual(self.diff_data.Dpar_err, Dpar)
self.assertEqual(self.diff_data.Dper_err, Dper)
self.assertEqual(self.diff_data.Dratio_err, Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_err.tostring(), Dpar_unit.tostring())
def test_set_spheroid_params(self):
"""Test the setting of spheroidal diffusion tensor parameters.
The following parameters will be set:
- tm: 20 ns
- Da: 2e6
- theta: 60 degrees
- phi: 290 degrees
"""
# The parameter values.
tm = 2e-8
Da = 2e6
theta = (60 / 360.0) * 2.0 * pi
phi = (290 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the diffusion parameters.
self.diff_data.set(param='tm', value=tm)
self.diff_data.set(param='Da', value=Da)
self.diff_data.set(param='theta', value=theta)
self.diff_data.set(param='phi', value=phi)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm, tm)
self.assertEqual(self.diff_data.Da, Da)
self.assertEqual(self.diff_data.theta, theta)
self.assertEqual(self.diff_data.phi, phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso, Diso)
self.assertEqual(self.diff_data.Dpar, Dpar)
self.assertEqual(self.diff_data.Dper, Dper)
self.assertEqual(self.diff_data.Dratio, Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit.tostring(), Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag.tostring(), tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation.tostring(), rotation.tostring())
self.assertEqual(self.diff_data.tensor.tostring(), tensor.tostring())
def test_set_spheroid_sim(self):
"""Test the setting of Monte Carlo simulation spheroidal diffusion tensor parameters.
Firstly the following parameters will be appended to empty lists:
- tm: 2 ns
- Da: 1e5
- theta: 0 degrees
- phi: 360 degrees
These MC sim values will then be explicity overwritten by setting the first elements of the
lists to:
- tm: 0.5 ns
- Da: 3e5
- theta: 2 degrees
- phi: 0 degrees
"""
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the number of MC sims.
self.diff_data.set_sim_num(1)
# Set the initial values.
self.diff_data.set(param='tm', value=2e-9, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=1e5, category='sim', sim_index=0)
self.diff_data.set(param='theta', value=0.0, category='sim', sim_index=0)
self.diff_data.set(param='phi', value=2.0 * pi, category='sim', sim_index=0)
# The new MC sim parameter values.
tm = 0.5e-9
Da = 3e5
theta = (2 / 360.0) * 2.0 * pi
phi = 0.0
# Set the MC sim parameter values (overwriting the initial values).
self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0)
self.diff_data.set(param='theta', value=theta, category='sim', sim_index=0)
self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_sim[0], tm)
self.assertEqual(self.diff_data.Da_sim[0], Da)
self.assertEqual(self.diff_data.theta_sim[0], theta)
self.assertEqual(self.diff_data.phi_sim[0], phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_sim[0], Diso)
self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
self.assertEqual(self.diff_data.Dper_sim[0], Dper)
self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(), Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(), tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation_sim[0].tostring(), rotation.tostring())
self.assertEqual(self.diff_data.tensor_sim[0].tostring(), tensor.tostring())
def test_set_tm(self):
"""Test the setting of the tm parameter.
The tm parameter will be set to 10 ns. The setting of tm should automatically create the
Diso parameter.
"""
# Set the diffusion type.
self.diff_data.set(param='type', value='sphere')
# Set the tm value to 10 ns.
self.diff_data.set(param='tm', value=1e-8)
# Test that the tm parameter has been set correctly.
self.assert_(hasattr(self.diff_data, 'tm'))
self.assertEqual(self.diff_data.tm, 1e-8)
# Test that the Diso parameter has been set correctly.
self.assert_(hasattr(self.diff_data, 'Diso'))
self.assertEqual(self.diff_data.Diso, 1/(6*1e-8))
class Test_diff_tensor(TestCase):
"""Unit tests for the data.diff_tensor relax module."""
def calc_spheroid_objects(self, tm, Da, theta, phi):
"""Function for calculating the spheroidal diffusion tensor objects."""
# The parameter values.
Diso = 1 / (6 * tm)
Dpar = Diso + 2.0 / 3.0 * Da
Dper = Diso - 1.0 / 3.0 * Da
Dratio = Dpar / Dper
# Vectors.
Dpar_unit = array(
[sin(theta) * cos(phi),
sin(theta) * sin(phi),
cos(theta)])
# Matrices.
if Dpar > Dper:
axis = array([0, 0, 1], float64)
tensor_diag = array([[Dper, 0.0, 0.0], [0.0, Dper, 0.0],
[0.0, 0.0, Dpar]])
else:
axis = array([1, 0, 0], float64)
tensor_diag = array([[Dpar, 0.0, 0.0], [0.0, Dper, 0.0],
[0.0, 0.0, Dper]])
# The rotation.
rotation = zeros((3, 3), float64)
two_vect_to_R(Dpar_unit, axis, rotation)
# The diffusion tensor.
tensor = dot(rotation, dot(tensor_diag, transpose(rotation)))
# Return the objects.
return Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor
def setUp(self):
"""Set 'self.diff_data' to an empty instance of the DiffTensorData class."""
self.diff_data = DiffTensorData()
def test_append_spheroid_sim(self):
"""Test the appending of Monte Carlo simulation spheroidal diffusion tensor parameters.
The following parameters will be appended to empty lists:
- tm: 8 ns
- Da: -1e7
- theta: 150 degrees
- phi: 30 degrees
"""
# The MC sim parameter values.
tm = 8e-9
Da = -1e7
theta = (150 / 360.0) * 2.0 * pi
phi = (30 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='oblate')
# Set the number of MC sims.
self.diff_data.set_sim_num(1)
# Set the initial values.
self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0)
self.diff_data.set(param='theta',
value=theta,
category='sim',
sim_index=0)
self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_sim[0], tm)
self.assertEqual(self.diff_data.Da_sim[0], Da)
self.assertEqual(self.diff_data.theta_sim[0], theta)
self.assertEqual(self.diff_data.phi_sim[0], phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(
tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_sim[0], Diso)
self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
self.assertEqual(self.diff_data.Dper_sim[0], Dper)
self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(),
Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation_sim[0].tostring(),
rotation.tostring())
self.assertEqual(self.diff_data.tensor_sim[0].tostring(),
tensor.tostring())
def test_display(self):
"""Test that the contents of the diffusion tensor object can be displayed."""
print(self.diff_data)
def test_set_Diso(self):
"""Test that the Diso parameter cannot be set."""
# Assert that a RelaxError occurs when Diso is set (to the tm value of 10 ns).
self.assertRaises(RelaxError, setattr, self.diff_data, 'Diso',
1 / (6 * 1e-8))
# Make sure that the Diso parameter has not been set.
self.assert_(not hasattr(self.diff_data, 'Diso'))
def test_set_spheroid_errors(self):
"""Test the setting of spheroidal diffusion tensor parameter errors.
The following parameter errors will be set:
- tm: 1 ns
- Da: 1e3
- theta: 3 degrees
- phi: 5 degrees
"""
# The parameter errors.
tm = 1e-8
Da = 1e3
theta = (3 / 360.0) * 2.0 * pi
phi = (5 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the diffusion parameter errors.
self.diff_data.set(param='tm', value=tm, category='err')
self.diff_data.set(param='Da', value=Da, category='err')
self.diff_data.set(param='theta', value=theta, category='err')
self.diff_data.set(param='phi', value=phi, category='err')
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_err, tm)
self.assertEqual(self.diff_data.Da_err, Da)
self.assertEqual(self.diff_data.theta_err, theta)
self.assertEqual(self.diff_data.phi_err, phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(
tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_err, Diso)
self.assertEqual(self.diff_data.Dpar_err, Dpar)
self.assertEqual(self.diff_data.Dper_err, Dper)
self.assertEqual(self.diff_data.Dratio_err, Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_err.tostring(),
Dpar_unit.tostring())
def test_set_spheroid_params(self):
"""Test the setting of spheroidal diffusion tensor parameters.
The following parameters will be set:
- tm: 20 ns
- Da: 2e6
- theta: 60 degrees
- phi: 290 degrees
"""
# The parameter values.
tm = 2e-8
Da = 2e6
theta = (60 / 360.0) * 2.0 * pi
phi = (290 / 360.0) * 2.0 * pi
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the diffusion parameters.
self.diff_data.set(param='tm', value=tm)
self.diff_data.set(param='Da', value=Da)
self.diff_data.set(param='theta', value=theta)
self.diff_data.set(param='phi', value=phi)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm, tm)
self.assertEqual(self.diff_data.Da, Da)
self.assertEqual(self.diff_data.theta, theta)
self.assertEqual(self.diff_data.phi, phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(
tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso, Diso)
self.assertEqual(self.diff_data.Dpar, Dpar)
self.assertEqual(self.diff_data.Dper, Dper)
self.assertEqual(self.diff_data.Dratio, Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit.tostring(),
Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag.tostring(),
tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation.tostring(),
rotation.tostring())
self.assertEqual(self.diff_data.tensor.tostring(), tensor.tostring())
def test_set_spheroid_sim(self):
"""Test the setting of Monte Carlo simulation spheroidal diffusion tensor parameters.
Firstly the following parameters will be appended to empty lists:
- tm: 2 ns
- Da: 1e5
- theta: 0 degrees
- phi: 360 degrees
These MC sim values will then be explicity overwritten by setting the first elements of the
lists to:
- tm: 0.5 ns
- Da: 3e5
- theta: 2 degrees
- phi: 0 degrees
"""
# Set the diffusion type.
self.diff_data.set(param='type', value='spheroid')
self.diff_data.set(param='spheroid_type', value='prolate')
# Set the number of MC sims.
self.diff_data.set_sim_num(1)
# Set the initial values.
self.diff_data.set(param='tm', value=2e-9, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=1e5, category='sim', sim_index=0)
self.diff_data.set(param='theta',
value=0.0,
category='sim',
sim_index=0)
self.diff_data.set(param='phi',
value=2.0 * pi,
category='sim',
sim_index=0)
# The new MC sim parameter values.
tm = 0.5e-9
Da = 3e5
theta = (2 / 360.0) * 2.0 * pi
phi = 0.0
# Set the MC sim parameter values (overwriting the initial values).
self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0)
self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0)
self.diff_data.set(param='theta',
value=theta,
category='sim',
sim_index=0)
self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0)
# Test the set values.
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_sim[0], tm)
self.assertEqual(self.diff_data.Da_sim[0], Da)
self.assertEqual(self.diff_data.theta_sim[0], theta)
self.assertEqual(self.diff_data.phi_sim[0], phi)
# Calculate the diffusion tensor objects.
Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(
tm, Da, theta, phi)
# Test the automatically created values.
self.assertEqual(self.diff_data.Diso_sim[0], Diso)
self.assertEqual(self.diff_data.Dpar_sim[0], Dpar)
self.assertEqual(self.diff_data.Dper_sim[0], Dper)
self.assertEqual(self.diff_data.Dratio_sim[0], Dratio)
# Test the vectors.
self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(),
Dpar_unit.tostring())
# Test the matrices.
self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(),
tensor_diag.tostring())
self.assertEqual(self.diff_data.rotation_sim[0].tostring(),
rotation.tostring())
self.assertEqual(self.diff_data.tensor_sim[0].tostring(),
tensor.tostring())
def test_set_tm(self):
"""Test the setting of the tm parameter.
The tm parameter will be set to 10 ns. The setting of tm should automatically create the
Diso parameter.
"""
# Set the diffusion type.
self.diff_data.set(param='type', value='sphere')
# Set the tm value to 10 ns.
self.diff_data.set(param='tm', value=1e-8)
# Test that the tm parameter has been set correctly.
self.assert_(hasattr(self.diff_data, 'tm'))
self.assertEqual(self.diff_data.tm, 1e-8)
# Test that the Diso parameter has been set correctly.
self.assert_(hasattr(self.diff_data, 'Diso'))
self.assertEqual(self.diff_data.Diso, 1 / (6 * 1e-8))
